title: Plasma miRNA-seq at ET0 of BP YFC-120 [YFC-120-1]


title: LIDAR, total, testis, b1

status: Public on May 14 2024

type: SRA

city: Philadelphia

first: Emily

last: Shields

state: Pennsylvania

address: 3400 Civic Center Blvd

country: USA

institute: University of Pennsylvania

library_source: transcriptomic

data_processing:
For LIDAR, LIDAR3 and NEB samples: Adapter trimming with TrimGalore v0.6.4: --length 5 --paired --retain_unpaired -r 20 -r 100. For NEB samples, additional trimming step with Cutadapt v 4.2: cutadapt -A GATCGTCGG --minimum-length 5 --paired-filter any
Samples with UMI (LIDAR, LIDAR-3): UMIs were extracted using umi_tools v1.1.2 with the regex ".*(?<umi_1>.{7})CG(?P<umi_2>.{2})AG(?P<umi_3>.{2})GGG" and remaining constant bases were trimmed with Cutadapt (cutadapt --minimum-length 5 -g CGAGGGG), then TSO dimers were removed with Cutadapt (cutadapt -e 3 -b CGTCAGATGTGTATAAGAGACAG --discard-trimmed)
Reads were mapped sequentially with STAR v2.7.10a to consensus rRNA repeats (BK000964.3), snoRNA from GENCODE vM27, snRNA from GENCODE vM27, piRNA from piRbase v3.0 using bowtie2 ver2.5.0, and tRNA from GtRNAdb and tRNAscan-SE as curated by Nedialkova et al. using GSNAP ver 2019-02-26 with SNP database provided, then to a custom GRCm39 genome with all of the sequences above masked and provided as extra scaffolds, using STAR (paired reads with inserts > 100nt) or bowtie2 (paired reads with inserts < 100nt and single reads)
Samples with UMI (LIDAR, LIDAR-3): bam files were deduplicated using umi_tools dedup with method --unique
Only reads with fragment length >=15 were retained for downstream analysis
Assembly: GRCm39
Supplementary files format and content: tab delimited files include raw counts corresponding to each gene (counts.genes.txt) or biotype, including reads mapped to non-annotation regions (counts.biotypes.txt)

molecule: total RNA

organism: Mus musculus

source_name: mouse testis

extract_protocol:
LIDAR and LIDAR-3 library preparation: The desired amount of total and fractionated RNAs was diluted to 1μl and mixed with 0.4μl of 10μM LIDAR_RT_primer (/5Biosg/GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGNNNNND). To anneal the LIDAR_RT_primer to the template RNA, samples were heated to 65°C for 5 min, then temperature was lowered to 4°C (0.5°C/s). To initiate retrotranscription, 6.28μl of RT_mix [25mM Tris-HCl pH=8.3, 20mM NaCl, 2.5mM MgCl2, 8mM DTT, 5% PEG-8000, 0.5mM dNTPs, 1mM GTP, 0.5 U/μl Murine RNase inhibitor, and 2U/μl Maxima H-minus Reverse Transcriptase – concentrations refer to a final volume of 8 μl] were added and samples were incubated at 25°C for 10 min. To further promote cDNA synthesis and template switch, temperature was raised to 42°C, 0.32μl of 50μM LIDAR_TSO_mix (equimolar ratio of the following oligos: /5Biosg/CGTCAGATGTGTATAAGAGACAGtgNNcgNNagNNrGrGrG, /5Biosg/CGTCAGATGTGTATAAGAGACAGvhNNcgNNagNNrGrGrG, /5Biosg/CGTCAGATGTGTATAAGAGACAGvhgNNcgNNagNNrGrGrG, /5Biosg/CGTCAGATGTGTATAAGAGACAGvhtgNNcgNNagNNrGrGrG, /5Biosg/CGTCAGATGTGTATAAGAGACAGvhmtgNNcgNNagNNrGrGrG) were added, and samples were incubated at 42°C for 80 min, followed by 10 cycles at 50°C for 2 min and 42°C for 2 min, then at 85°C for 5 min. To pre-amplify and add adapters to cDNA, 12μl of KAPA_mix [1X KAPA HiFi HotStart buffer Ready Mix, 0.5μM LIDAR_preamp_f (TCGTCGGCAGCGTCAGATGTGTATAAGAGAC*A*G), and 0.1μM LIDAR_preamp_r (GTCTCGTGGGCTCGGAGA) – concentrations refer to a final volume of 20 μl]  were added and samples were incubated with the following PCR cycling conditions: denaturation (95°C for 3 min), 18 cycles of amplification (98°C for 20s, 70°C for 30s, 72°C for 30s), final extension (72°C for 5 min). Quality of adapter-containing libraries was assessed by loading 5ul on a 2% agarose gel. To generate the final libraries, 2μl of pre-amplified were diluted to 37μl with 10mM Tris-HCl pH=8, 0.5μl of each 10μM custom Nextera indexing primers was added, followed by 12μl of Q5_mix [1X Q5 buffer, 0.5mM dNTPs, 0.02 U/µl Q5 High-Fidelity DNA Polymerase (Cat. No M0491, New England Biolabs) – concentrations refer to a final volume of 50 μl]. Samples were incubated with the following PCR cycling conditions: denaturation (98°C for 30 sec), 18 cycles of amplification (98°C for 10s, 65°C for 20s, 72°C for 20s), final extension (72°C for 2 min). Indexed libraries were purified using 2.3X SPRI beads and eluted in 50μl of TE buffer (10mM Tris-HCl pH=8, 1mM EDTA).
For LIDAR-3, the LIDAR-3_RT_oligo was generated by mixing equimolar amounts of LIDAR-3_RT_sense (/5Biosg/GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGNNNNNN) and LIDAR-3_RT_antisense (CdUGdUCdUCdUdUAdUACACAdUCdUCCGAG/3ddC/), followed by heating at 95°C for 5 min, and a slow cool down to 25°C (0.1°C/s). To prepare LIDARsp libraries, 1μl of input RNA was first denatured at 70°C for 2 min, then temperature was lowered to 50°C and 0.4μl of 1μM LIDAR-3_RT_oligo were added. Samples were incubated at 50°C for further 2min, then temperature was lowered to 4°C (0.5°C/s). To initiate retrotranscription, 6.28μl of RT_mix were added and samples were incubated at 25°C for 10 min. To further promote cDNA synthesis and template switch, temperature was raised to 42°C, 0.32μl of 50μM LIDAR_TSO_mix were added, and samples were incubated at 50°C for 80 min, followed by 10 cycles at 55°C for 2 min and 50°C for 2 min, then at 85°C for 5 min. LIDAR-3_RT_antisense was digested by adding 1ul of USER II enzyme and incubating at 37°C for 30 min. USER II was heat inactivated by incubation at 65°C for 10 min. To pre-amplify and add adapters to cDNA, 12μl of KAPAsp_mix [1X KAPA HiFi HotStart buffer Ready Mix, 2μM LIDAR_preamp_f (TCGTCGGCAGCGTCAGATGTGTATAAGAGAC*A*G), and 0.5μM LIDAR_preamp_r (GTCTCGTGGGCTCGGAGA) – concentrations refer to a final volume of 20 μl] were added and samples were incubated with the following PCR cycling conditions: denaturation (95°C for 3 min), 6 cycles of 3-step amplification (98°C for 20s, 63°C for 30s, 72°C for 30s), 12 cycles of 2-step amplification (98°C for 20s, 72°C for 50s), final extension (72°C for 5 min). Quality of adapter-containing libraries was assessed by loading 5ul on a 2% agarose gel. To generate the final libraries, 2μl of pre-amplified were diluted to 37μl with 10mM Tris-HCl pH=8, 1μl of each 10μM custom Nextera indexing primers was added, followed by 12μl of Q5sp_mix [1X Q5 buffer, 0.5mM dNTPs, 0.02 U/µl Q5 High-Fidelity DNA Polymerase – concentrations refer to a final volume of 50 μl]. Samples were incubated with the following PCR cycling conditions: denaturation (98°C for 30 sec), 7 cycles of amplification (98°C for 10s, 65°C for 20s, 72°C for 20s), final extension (72°C for 5 min). Indexed libraries were purified using 2.4X SPRI beads and eluted in 50μl of TE buffer (10mM Tris-HCl pH=8, 1mM EDTA).
Small RNA-seq and mRNA-seq library preparation
Small RNA libraries were prepared using the NEBnext Small RNA Library Prep Set for Illumina (Cat. No E7330S, New England Biolabs), following the standard protocol with the following parameters: 1) 1:2 dilution of 3’SR Adaptor, SR RT Primer, and 5’SR Adaptor 2) 15 indexing PCR cycles 3) cleanup of final libraries with QIAgen MinElute PCR purification kit, followed by a second cleanup with 2X SPRI. Libraries were analyzed on a 6% non-denaturing polyacrylamide gel.
For mRNA-seq libraries, polyA RNA was enriched from 2 μg total RNA using Dynabeads Oligo(dT)25. Poly-A-enriched fraction was used for library construction using the NEBnext Ultra II Directional Library Prep Kit for Illumina (Cat. No. E7760L, New England Biolabs), following the standard protocol but using half the reaction volumes recommended. Libraries were analyzed on a 2% agarose gel.
Both small RNA-seq and mRNA-seq libraries were quantified using NEBNext Library Quant Kit for Illumina (Cat. No E7630L, New England Biolabs). Libraries were sequenced on an Illumina NextSeq500 instrument.

treatment_protocol: C57BL/6 mouse embryonic stem cells (ESC) were purchased from ATCC (SCRC-1002) and maintained onto 1% gelatin-coated dishes in DMEM knockout medium supplemented with 15% ES-grade Fetal Bovine Serum, 1% GlutaMAX, 1% Non-essential aminoacids, 0.5% Penicillin/Streptomycin solution, 110μM β-mercaptoethanol, 100 units/ml Leukemia Inhibitory Factor (LIF), 3μM GSK-3 Inhibitor XVI, 1 μM MEK1/2 Inhibitor III. Cells were passaged through trypsinization (0.05%) every 2–3 days. Prior to neuronal progenitor cells (NPC) differentiation, embryonic stem cells that were maintained in N2B27 serum-free medium consisting of 1:1 mix of Neurobasal medium and DMEM/F12, supplemented with 1X N2, 1X B27, 1% GlutaMAX, 1% Non-essential aminoacids, 0.5% Penicillin/Streptomycin, 55μM β-mercaptoethanol, 100 units/ml Leukemia Inhibitory Factor (LIF), 3μM GSK-3 Inhibitor XVI, 1 μM MEK1/2 Inhibitor III. For NPC differentiation differentiation, Epiblast-like cells (EpiLC) were induced from ESC in N2B27 serum-free medium (without 2i and LIF) supplemented with 40μg/ml of BSA, and 10ng/ml bFGF for 72h. EpiLC were treated with 500nM SAG in N2B27 serum-free medium (without 2i and LIF) for 48h to generate NPC.

tag: tissue

value: mouse testis

tag: input amount_(ng)


title: LIDAR, total, brain, b3

source_name: mouse brain

value: mouse brain


title: LIDAR, total, brain, b1


title: LIDAR, total, brain, b2


title: Gentamicin 20 min, RpoB ChIP-seq

status: Public on May 15 2024

city: Beijing

first: Ruochen

last: Chai

address: Haidian District

country: China

institute: Tsinghua University

library_source: genomic

data_processing:
We performed the same steps as before, including quality control, adapter trimming, and sequence alignment. For the ChIP-seq and DNA input control libraries, we used bedtools genomecov with the '-pc' option to calculate the coverage at each nucleotide position, and normalize it to reads per million. To reduce noise, we excluded positions with coverage less than 5. Finally, we divided the read counts at each nucleotide position in the ChIP-seq data by the read counts at the corresponding position in the input DNA control, yielding the ChIP-seq signal of RpoB and Gam. To perform Gam peak calling, we filtered for candidate regions based on the following criteria: Normalized coverage per nucleotide ≥ 1.3, and the region width ≥ 250 bp. Then, all peak locations in each library was compiled into a BED file. Finally, we merged the filtered lists from all four time points (0 minutes, 20 minutes, 40 minutes, and 60 minutes) by bedtools merge (v2.30.0) with default parameters, and generated a final set of 355 Gam peak locations.
Assembly: NC_000913.3
Supplementary files format and content: txt file for coevrage per base and bed file for peak annotation.

molecule: genomic DNA

organism: Escherichia coli

source_name: BW25113 lacYI::lacIAM-Ptac-gam-3xFLAG

growth_protocol: The overnight seed culture of BW25113 lacYI::lacIAM-Ptac-gam-3xFLAG was diluted 1:350 with fresh LB medium. When the culture grew to OD600~0.4, it was further diluted 1:50 into 200 ml of LB supplemented with 80 μM IPTG (Sigma, V900917). Once the culture reached an OD600 of 0.5, a 40 ml culture was taken as the 0 min sample.

extract_protocol:
The Cells were harvest by spin at 5,000 g for 3 min, and washed once with 20 ml PBS. The washed cell pellets were then resuspended in 1% paraformaldehyde (Beyotime, P0099) diluted by PBS (5 ml for 40 ml culture of OD600~0.5, with the volume adjusted accordingly), and incubated at 25 °C for 30 min with rotation to perform crosslinking. The fixation reaction was quenched by adding Glycine-HCl (Solarbio, G8200; Sigma, 320331) solution to a final concentration of 125 mM. The fixed cells were collected and washed twice with 10 ml TBS (50 mM Tris HCl, 150 mM NaCl, pH 7.4), and then frozen by liquid nitrogen and stored at -80 °C before use. The thawed pellets were resuspended with 1.1 ml TBS supplemented with proteinase inhibitor (Thermo Fisher, A32955), and sonicated on ice until the resuspensions turned clear. After spin at 12,000 g for 10 min, the supernatant of lysates was transferred to a new tube. Each lysate was split into a DNA input control (0.1 ml) and immunoprecipitation (IP) samples for Gam-3xFLAG ChIP (0.5 ml) and RpoB ChIP (0.5 ml). For the RpoB ChIP experiments, 8 μl of anti-RpoB antibody (Abcam, ab191598) was added to the IP lysate and incubated overnight at 4 °C with rotation. Next, 20 μl of Dynabeads Protein G (Thermo Fisher, 10003D) were added to the IP-RpoB lysate and incubated for 3 h at 4 °C with rotation. The beads were pelleted using a magnetic rack, and washed three times with 0.2 ml of TBS. During the last wash, the resuspension was transferred to a new tube before discarding the supernatant. Elution was performed by resuspending the washed beads in 70 ml of 50 mM Glycine-HCl (pH 2.8). After a 2-min incubation, the eluate was carefully collected. The elution was performed twice, and the eluates were combined. Finally, 15 μl of 1M Tris (pH 8.0) was then added to neutralize the pH. For the Gam-3xFLAG ChIP experiments, 20 μl ANTI-FLAG M2 magnetic beads (Sigma, M8823) were added to another IP lysate and incubated for 2 h at 4 °C with rotation. The beads were then washed and eluted as stated in the RpoB ChIP experiment.  Together with the DNA input control, we incubated the eluates from RpoB ChIP and Gam-3xFLAG ChIP at 65 °C overnight with mild shaking, supplementing with Proteinase K at a final concentration of 0.4 mg/ml. We then extracted the DNA from those samples using the MasterPure Complete DNA/RNA Purification Kit, and measured the concentration with the Qubit 1xdsDNA HS Assay Kit.
For library construction, we used the same process as described in the genome re-sequencing, but input 5 ng DNA per sample and scaled down the tagmentation system accordingly.

treatment_protocol: Gentamicin was then added to the remaining culture to a final concentration of 6 μg/ml and mixed thoroughly.

tag: cell line

value: BW25113 lacYI::lacIAM-Ptac-gam-3xFLAG

tag: treatment

value: 6 mg/L, gentamicin


title: nanoPARE: TIL25-0.4mm-rep1

city: Wuhan

first: Junpeng

last: Zhan

state: Hubei

address: 1 Shizishan Street, Hongshan District

institute: Huazhong Agricultural University

description:
cleavage_sites_miRNA_TIL25_0.4mm_1.tsv.gz
cleavage_sites_phasiRNA_TIL25_0.4mm_1.tsv.gz

data_processing:
Small RNA-transcript interactions in each anther sample were identified using the previously published nanoPARE analysis pipeline.
Assembly: Respective reference genomes of Zea varieties
Supplementary files format and content: Tables of cleavage sites

molecule: polyA RNA

organism: Zea mays subsp. mexicana

source_name: anther

extract_protocol:
Fresh anthers were snap-frozen in liquid nitrogen and total RNA was extracted using the TRI reagent (Sigma-Aldrich).
RNA-seq (Smart-seq2) and nanoPARE libraries were prepared from 5 ng total RNA per sample using the nanoPARE library preparation protocol.

tag: group

tag: cell type

value: anther

tag: genotype

tag: molecule subtype

value: polyA RNA - 5' end


title: nanoPARE: TIL25-1.5mm-rep1

description:
cleavage_sites_miRNA_TIL25_1.5mm_1.tsv.gz
cleavage_sites_phasiRNA_TIL25_1.5mm_1.tsv.gz


title: nanoPARE: TIL25-0.4mm-rep3

description:
cleavage_sites_miRNA_TIL25_0.4mm_3.tsv.gz
cleavage_sites_phasiRNA_TIL25_0.4mm_3.tsv.gz


title: nanoPARE: TIL25-1.5mm-rep2

description:
cleavage_sites_miRNA_TIL25_1.5mm_2.tsv.gz
cleavage_sites_phasiRNA_TIL25_1.5mm_2.tsv.gz


title: 0 min, RpoB ChIP-seq


title: nanoPARE: TIL25-0.4mm-rep2

description:
cleavage_sites_miRNA_TIL25_0.4mm_2.tsv.gz
cleavage_sites_phasiRNA_TIL25_0.4mm_2.tsv.gz


title: Smart-seq2: TIL25-1.5mm-rep1

value: polyA RNA - transcript body


title: Smart-seq2: TIL25-1.5mm-rep3


title: Smart-seq2: TIL25-0.4mm-rep3


title: Smart-seq2: TIL25-1.5mm-rep2


title: Smart-seq2: TIL25-0.4mm-rep2


title: NEB, total, brain, b3


title: small RNA-seq: TIL25-1.5mm-rep3

data_processing:
To quantify phasiRNA abundance, sRNA-seq reads were mapped to the respective Zea genomes using Bowtie v1.3.1; to quantify miRNA abundance, sRNA-seq reads were mapped to a FASTA file of all mature miRNAs annotated for each genome using bowtie; and to quantify mRNA abundance, Smart-seq2 reads were mapped to the respective Zea genomes (B73 RefGen_v5 was used for the ago18 mutant data) using HISAT v2.1.0. Reads mapped to PHAS loci or miRNAs were counted using featureCounts v1.6.3 and normalized to counts per million (CPM) using edgeR v4.0.2. Differential expression analyses were performed using edgeR with a generalized linear model-based method. Small RNA-transcript interactions in each anther sample were identified using the nanoPARE analysis pipeline (Schon et al., 2018). The sRNA-target pairs with adjusted P value < 0.05 at the EndCut step and are detected in at least two biological replicates were considered positive.
Assembly: Respective reference genomes of Zea varieties
Supplementary files format and content: CPM tables for sRNA-seq and RNA-seq, cleavage-site tables for nanoPARE

extract_protocol:
Fresh anthers were snap-frozen in liquid nitrogen and total RNA was extracted using the TRI reagent (Sigma-Aldrich) or the TraPR Small RNA Isolation kit (Lexogen; for TraPR sRNA-seq only)
sRNA-seq libraries were prepared from ~100 ng total RNA per sample using a Somagenics RealSeq-AC miRNA library kit following the manufacturer’s protocol. RNA-seq (Smart-seq2) and nanoPARE libraries were prepared from 5 ng total RNA per sample using the nanoPARE library preparation protocol.

value: small RNA - total


title: small RNA-seq: TIL25-1.5mm-rep1


title: small RNA-seq: TIL25-0.4mm-rep2


title: Smart-seq2: TIL25-0.4mm-rep1


title: small RNA-seq: TIL25-0.4mm-rep3


title: small RNA-seq: TIL25-0.4mm-rep1


title: nanoPARE: TIL11-1mm-rep3

description:
cleavage_sites_miRNA_TIL11_1mm_3.tsv.gz
cleavage_sites_phasiRNA_TIL11_1mm_3.tsv.gz

organism: Zea mays subsp. parviglumis


title: nanoPARE: TIL11-2mm-rep2

description:
cleavage_sites_miRNA_TIL11_2mm_2.tsv.gz
cleavage_sites_phasiRNA_TIL11_2mm_2.tsv.gz


title: nanoPARE: TIL11-1mm-rep2

description:
cleavage_sites_miRNA_TIL11_1mm_2.tsv.gz
cleavage_sites_phasiRNA_TIL11_1mm_2.tsv.gz


title: nanoPARE: TIL11-2mm-rep3

description:
cleavage_sites_miRNA_TIL11_2mm_3.tsv.gz
cleavage_sites_phasiRNA_TIL11_2mm_3.tsv.gz


title: nanoPARE: TIL11-1mm-rep1

description:
cleavage_sites_miRNA_TIL11_1mm_1.tsv.gz
cleavage_sites_phasiRNA_TIL11_1mm_1.tsv.gz


title: nanoPARE: TIL25-1.5mm-rep3

description:
cleavage_sites_miRNA_TIL25_1.5mm_3.tsv.gz
cleavage_sites_phasiRNA_TIL25_1.5mm_3.tsv.gz


title: nanoPARE: TIL11-2mm-rep1

description:
cleavage_sites_miRNA_TIL11_2mm_1.tsv.gz
cleavage_sites_phasiRNA_TIL11_2mm_1.tsv.gz


title: nanoPARE: TIL11-1.5mm-rep3

description:
cleavage_sites_miRNA_TIL11_1.5mm_3.tsv.gz
cleavage_sites_phasiRNA_TIL11_1.5mm_3.tsv.gz


title: nanoPARE: TIL11-1.5mm-rep2

description:
cleavage_sites_miRNA_TIL11_1.5mm_2.tsv.gz
cleavage_sites_phasiRNA_TIL11_1.5mm_2.tsv.gz


title: nanoPARE: TIL11-1.5mm-rep1

description:
cleavage_sites_miRNA_TIL11_1.5mm_1.tsv.gz
cleavage_sites_phasiRNA_TIL11_1.5mm_1.tsv.gz


title: nanoPARE: TIL11-0.7mm-rep3

description:
cleavage_sites_miRNA_TIL11_0.7mm_3.tsv.gz
cleavage_sites_phasiRNA_TIL11_0.7mm_3.tsv.gz


title: nanoPARE: TIL11-0.7mm-rep2

description:
cleavage_sites_miRNA_TIL11_0.7mm_2.tsv.gz
cleavage_sites_phasiRNA_TIL11_0.7mm_2.tsv.gz


title: nanoPARE: TIL11-0.7mm-rep1

description:
cleavage_sites_miRNA_TIL11_0.7mm_1.tsv.gz
cleavage_sites_phasiRNA_TIL11_0.7mm_1.tsv.gz


title: nanoPARE: TIL11-0.4mm-rep1

description:
cleavage_sites_miRNA_TIL11_0.4mm_1.tsv.gz
cleavage_sites_phasiRNA_TIL11_0.4mm_1.tsv.gz


title: nanoPARE: TIL11-0.4mm-rep2

description:
cleavage_sites_miRNA_TIL11_0.4mm_2.tsv.gz
cleavage_sites_phasiRNA_TIL11_0.4mm_2.tsv.gz


title: Smart-seq2: TIL11-2mm-rep3


title: small RNA-seq: TIL25-1.5mm-rep2


title: Smart-seq2: TIL11-2mm-rep2


title: Smart-seq2: TIL11-2mm-rep1


title: Smart-seq2: TIL11-1mm-rep3


title: Smart-seq2: TIL11-0.7mm-rep3


title: Smart-seq2: TIL11-0.7mm-rep1


title: Smart-seq2: TIL11-1mm-rep2


title: Smart-seq2: TIL11-1.5mm-rep2


title: Smart-seq2: TIL11-0.7mm-rep2


title: Smart-seq2: TIL11-1.5mm-rep1


title: small RNA-seq: TIL11-2mm-rep3


title: small RNA-seq: TIL11-2mm-rep2


title: Smart-seq2: TIL11-0.4mm-rep1


title: Smart-seq2: TIL11-1.5mm-rep3


title: small RNA-seq: TIL11-2mm-rep1


title: Smart-seq2: TIL11-0.4mm-rep2


title: small RNA-seq: TIL11-1mm-rep3


title: small RNA-seq: TIL11-1mm-rep2


title: small RNA-seq: TIL11-1.5mm-rep1


title: small RNA-seq: TIL11-1.5mm-rep3


title: small RNA-seq: TIL11-1.5mm-rep2


title: small RNA-seq: TIL11-0.7mm-rep2


title: small RNA-seq: TIL11-1mm-rep1


title: small RNA-seq: TIL11-0.7mm-rep1


title: nanoPARE: RIL003-1.5mm-rep3

description:
cleavage_sites_miRNA_RIL003_1.5mm_3.tsv.gz
cleavage_sites_phasiRNA_RIL003_1.5mm_3.tsv.gz

organism: Zea luxurians


title: nanoPARE: RIL003-1.5mm-rep1

description:
cleavage_sites_miRNA_RIL003_1.5mm_1.tsv.gz
cleavage_sites_phasiRNA_RIL003_1.5mm_1.tsv.gz


title: small RNA-seq: TIL11-0.4mm-rep1


title: Smart-seq2: TIL11-1mm-rep1


title: nanoPARE: RIL003-1.5mm-rep2

description:
cleavage_sites_miRNA_RIL003_1.5mm_2.tsv.gz
cleavage_sites_phasiRNA_RIL003_1.5mm_2.tsv.gz


title: small RNA-seq: TIL11-0.7mm-rep3


title: small RNA-seq: TIL11-0.4mm-rep2


title: nanoPARE: RIL003-0.4mm-rep3

description:
cleavage_sites_miRNA_RIL003_0.4mm_3.tsv.gz
cleavage_sites_phasiRNA_RIL003_0.4mm_3.tsv.gz


title: nanoPARE: RIL003-0.4mm-rep1

description:
cleavage_sites_miRNA_RIL003_0.4mm_1.tsv.gz
cleavage_sites_phasiRNA_RIL003_0.4mm_1.tsv.gz


title: nanoPARE: RIL003-0.4mm-rep2

description:
cleavage_sites_miRNA_RIL003_0.4mm_2.tsv.gz
cleavage_sites_phasiRNA_RIL003_0.4mm_2.tsv.gz


title: Smart-seq2: RIL003-0.4mm-rep2


title: Smart-seq2: RIL003-0.7mm-rep2


title: Smart-seq2: RIL003-0.7mm-rep1


title: Smart-seq2: RIL003-1.5mm-rep3


title: Smart-seq2: RIL003-1.5mm-rep1


title: small RNA-seq: RIL003-1.5mm-rep3


title: small RNA-seq: RIL003-0.7mm-rep2


title: small RNA-seq: RIL003-1.5mm-rep2


title: Smart-seq2: RIL003-1.5mm-rep2


title: small RNA-seq: RIL003-0.7mm-rep1


title: Smart-seq2: RIL003-0.4mm-rep1


title: small RNA-seq: RIL003-0.4mm-rep2


title: small RNA-seq: RIL003-0.4mm-rep1


title: small RNA-seq: RIL003-0.4mm-rep3


title: ATAC-seq_WT_BM5_IL18Ra-ST2+PD1-IL17RB+

city: Chiba-shi

first: Arifumi

last: Iwata

state: Chiba

address: 1-8-1 Inohana, Chuou-ku

department: Department of Allergy and Clinical Immunology

country: Japan

institute: Chiba University

data_processing:
ATAC-seq data were aligned to mm10 genome assembly using Bowtie2 with paired-end mode. Mapped fragments were trimmed 4 bp from the start and 5 bp from the end using bedtools. The data were visualized and the peaks were identified using the HOMER package.
Assembly: mm10
Supplementary files format and content: bedgraph

source_name: Bone marrow

extract_protocol:
Lungs were cut into small pieces and digested in RPMI containing collagenase A and Dnase I using gentleMACS Dissociator and then passed through 70 µm filter. Lung ILC2s were sorted by SONY SH800. Bone marrow cells were harvested and lineage-positive cells were depleted using MojoSort Mouse Hematopoietic Progenitor Cell Isolation Kit. Each fraction of ILC2 lineages were sorted by BD Melody.
ATAC-seq library was generated using Omni-ATAC protocol.

value: Bone marrow

value: WT

value: no treatment


title: nanoPARE: RIL003-0.7mm-rep2

description:
cleavage_sites_miRNA_RIL003_0.7mm_2.tsv.gz
cleavage_sites_phasiRNA_RIL003_0.7mm_2.tsv.gz


title: ATAC-seq_WT_BM4_IL18Ra+ST2+PD1-IL17RB+


title: ATAC-seq_WT_BM3_IL18Ra+ST2-PD1-IL17RB+


title: ATAC-seq_WT_BM2_IL18Ra+ST2-PD1+IL17RB+


title: ATAC-seq_G3SEKO_BM2_IL18Ra+ST2-PD1+IL17RB+


title: ATAC-seq_G3SEKO_BM3_IL18Ra+ST2-PD1-IL17RB+


title: ATAC-seq_G3SEKO_BM1_IL18Ra+ST2-PD1+IL17RB-


title: nanoPARE: RIL003-0.7mm-rep1

description:
cleavage_sites_miRNA_RIL003_0.7mm_1.tsv.gz
cleavage_sites_phasiRNA_RIL003_0.7mm_1.tsv.gz


title: Smart-seq2: RIL003-0.4mm-rep3


title: small RNA-seq: RIL003-1.5mm-rep1


title: Synthetic DNA Oligo

city: Santa Barbara

first: Alex

last: Chialastri

state: CA

address: 2002 BioEngineering Bldg, CNTR for Bioengineering

institute: University of California Santa Barbara

description:
Illumina HiSeq 4000 and Illumina NextSeq 500
Synthetic DNA Oligo containing a symmetrically methylated, hemimethylated, or hemi-hydroxymethylated CpG Dyad (3 Sequencing Run each Combined)

library_source: other

data_processing:
Illumina bcl2fastq2 v 2.20 software used for basecalling A custom Perl script was used to demultiplex genomic based read barcodes from RNA based read barcodes. This code is available on request. RNA enriched samples were processed for RNA transcripts, while unenriched samples were used to identify site specific 5mC as well as the status of CpG dyads as fully or hemi-methylated. For genomic site specific 5mC detection (for absolute 5mC (or 5hmC) level calling), exact duplicates were removed using Clumpify from BBTools. A custom Perl script was use to extract the single cell barcode and UMI from each read. Then read 1 and 2 were trimmed using TrimGalore in paired end mode. The 5’ end of read 1 was clipped by 20 bases and the 3’ end of read 2 was hard clipped 34 bases after detection of the PCR amplification sequence CCACATCACCCAAACC to remove potential bias from enzymatic digestion and to avoid recounting CpG dyad detections utilized in the maintenance measurement. The 5’ end of read 2 was clipped by 9 bases to remove potential bias from the linear amplification 9-mer. The 3’ end of read 1 was also hard clipped 9 bases after detection of the Illumina adapter was performed. Each read was mapped individually using Bismark v0.21.0 in conjunction with Bowtie2 v2.3.5 to MM10 or hg19 for mouse or human samples, respectively. Using Bismark, both resulting sam files were deduplicated further using UMI, cell barcode and mapping location. The bismark_methylation_extractor tool was then used to extract detected cytosines. After which custom Perl code was used to connect detected cytosines to their respective cell. CpG detection files from the same DNA strand for read 1 and read 2 were then combined and any duplicate detections where the same cytosine was read in both read 1 and read 2 were removed using the UMI. Custom codes for analyzing Dyad-seq data and the accompanying documentation is provided with this work. For genomic CpG Dyad specific calling (for 5mCpG (or 5hmC) maintenance calling), Read 1 was trimmed to 86 bases. Then exact duplicates were removed using Clumpify from BBTools. A custom Perl script was use to extract the single cell barcode and UMI from each read. Then read 1 was trimmed using the default settings of TrimGalore. Read 1 was mapped using Bismark v0.21.0 in conjunction with Bowtie2 v2.3.5 to MM10 or hg19 for mouse or human samples, respectively. Using Bismark, both resulting sam files were deduplicated further using UMI, cell barcode and mapping location. For library preparation using MspJI, a custom Perl script was used to identify 5mC positions in the genome as detected by MspJI and interrogate the methylation status of the opposing cytosine in a CpG or CpHpG dyad context from the nucleobase conversion. For library preparation using AbaSI, a custom Perl script was used to identify 5hmC positions in the genome as detected by AbaSI and interrogate the methylation status of the opposing cytosine in a CpG dyad context from the nucleobase conversion. For bulk RNA based reads, read 2 sequences were trimmed to 50 bases and mapped in the sense direction to the refseq MM10 transcriptome build supplemented with ERCC mRNA spike-in sequences using bwa v0.7.15 with parameters aln -q 0 -n 0.04 -k 2 -l 200 -t 6 -B 12. Any read mapping to multiple loci were distributed uniformly across those loci. Gene isoforms were consolidated into a gene count, and the UMI was used to deduplicate reads from each gene for each individual cell. The number of observations was converted into transcript counts based on binomial statistics as described previously by Grün et al.. Genes that were not detected in at least one cell were discarded from any downstream analysis. For single cell RNA based reads, Read 2 was trimmed using the default settings of TrimGalore. After trimming, STARsolo (STAR aligner version 2.7.8a) was used to map the reads to MM10 using the gene annotation file from Ensembl . The reads were again mapped to MM10 using the transposable elements annotation file described in TEtranscripts. Transcripts with the same UMI were deduplicated, transcripts detected from genes or transposable elements were analyzed together and any that were not detected in at least one cell were removed from any downstream analysis. Required code to go from raw FASTQ files to processed data can be found on github at https://github.com/alexchialastri/scDyad-T-seq
Assembly: MM10 and hg19
Supplementary files format and content: 5mCpG Dyad maintenance detection files [noted in the naming of the file as *_CGMaintained.txt (for loci detected as maintained {e.g. fully methylated dyads for M-M-Dyad-seq}) and *_CGNonMaintained.txt (for loci detected as not maintained {e.g. hemi-methylated dyads for M-M-Dyad-seq})] list detected methylated or unmethylated CpG maintenance sites. Column 1 is the cell number (in bulk this is the sample replicate indicator), column 2 is the chromosome (with chr23 indicating the X chromosome, chr24 indicating the Y chromosome, and chr25 indicating a mitocondrial based detection), column 3 is the genomic loci, column 4 is the UMI detected and column 4 is the strand of the detected mark.
Supplementary files format and content: Absolute 5mCpG detection files [noted in the naming of the file as *_BS-CpG_All.txt or *BS-CpG_All_BothStrands_Unique.txt] list detected methylated or unmethylated CpG sites. Column 1 is the cell number (in bulk this is the sample replicate indicator), column 2 is the chromosome (with chr23 indicating the X chromosome, chr24 indicating the Y chromosome, and chr25 indicating a mitocondrial based detection), column 3 is the genomic loci, column 4 is the the strand of the detected mark, column 5 is the UMI detected and column 6 indicates if the cytosine was methylated (Z) or unmethylated (z) . Supplementary_files_format_and_content: For Bulk samples RNA-seq gene count files (noted in the naming of the file as *-READ_COUNTS_c.txt.gz) is a matrix with the columns indicating sample (replicate) number, and each row indicating the number of counts detected for a given gene.
Supplementary files format and content: Single cell transcript counts contain 6 files. 3 refer to the detection of unique transcripts related to genes (*_Genes_matrix.mtx.gz, *_Genes_features.tsv.gz, and *_Genes_barcodes.tsv.gz) and 3 refer to the detection of unique transcripts related to transposable elements (*_TE_matrix.mtx.gz, *_TE_features.tsv.gz, and *_TE_barcodes.tsv.gz). These set of 3 files are in the standard 10x sparse data matrix format (Market Exchange Format). The *_barcodes.tsv.gz file gives the list of cell barcodes used in the experiment. Note: these are in alphabetical order and not ordered by cell number, see supplementary file ('SingleCell_barcodesOrdered.csv') on main page for which barcodes refer to what cell number. The *_features.tsv.gz file gives the list of gene or transposable elements names. The *_matrix.mtx.gz gives the location and value of non zero elements in gene or transposable elements detection matrix, with column 1 refering to the feature, column 2 to the cell number, and column 3 to the number of transcripts detected.
Library strategy: M-M-Dyad-seq

molecule: other

organism: synthetic construct

source_name: N/A (Synthetic DNA Oligo)

growth_protocol: All cells were maintained in incubators at 37°C and 5% CO2. Mouse embryonic stem cell line ES-E14TG2a (E14) were grown on gelatin (Millipore Sigma, ES-006-B) coated tissue culture plates with media containing high glucose DMEM (Gibco, 10569044), 1% non-essential amino acid (Gibco, 11140050), 1% Glutamax (Gibco, 35050061), 1x Penicillin-Streptomycin (Gibco, 15140122), and 15% stem cell qualified serum (Millipore Sigma, ES-009-B). The media was frozen in aliquots and used thereafter for a maximum of 2 weeks after thawing while storing it at 4°C. Once thawed, 1 µL of beta-mercaptoethanol (Gibco, 21985023), and 1 µL of LIF (Gibco, A35933) were added for every 1 mL of thawed media. Cells were washed with 1x DPBS (Gibco, 14190250) and the media was exchanged daily. Cells were routinely passaged 1:6 once they reached 75% confluency using 0.25% trypsin-EDTA (Gibco, 25200056). E14 cells grown under these conditions also describe the SL experimental group. For FACS sorting, a single-cell suspension was made using 0.25% trypsin-EDTA. The trypsin was then inactivated using serum containing medium. Afterwards, the cells were washed with 1x DPBS before being passed through a cell strainer and sorted for single cells into 384-well plates. K562 cells were grown in RPMI (Gibco, 61870036) with 10% serum (Gibco, 10437028) and 1x Penicillin-Streptomycin. When the culture reached a density of approximately 1 million cells per mL, they were split and resuspended at a density of 200,000 cells per mL. Cells were washed and FACS sorted as described for E14 cells.

extract_protocol: Bulk genomic DNA was extracted using the DNeasy kit (Qiagen, 69504) according to the manufacturer’s recommendations. Bulk total RNA was extracted using TRIzol reagent (Invitrogen, 15596018) according to the manufacturer’s recommendations. For single cell experiments, whole cell lysate was used by soring cells via FACs directly into lysis buffer. For all bulk Dyad-seq experiments, 100 ng of purified genomic DNA was resuspended in 20 µL of glucosylation mix (1x CutSmart buffer (NEB, B7204S), 2.5x UDP-glucose, 10 U T4-BGT (NEB, M0357L)) and the samples were incubated at 37°C for 16 hours. Afterwards, 10 µL of protease mix (100 µg protease (Qiagen, 19155), 1x CutSmart buffer) was added to each sample, and the samples were heated to 50°C for 5 hours, 75°C for 20 minutes, and 80°C for 5 minutes. After this, processing of the samples differed based on the version of Dyad-seq used. For M-M-Dyad-seq and M-H-Dyad-seq, 10 µL of MspJI digestion mix (2 U MspJI, 1x enzyme activator solution, 1x CutSmart buffer) was added to each sample and the samples were heated to 37°C for 5 hours, and 65°C for 20 minutes. Next, 1 µL of barcoded 1 µM double-stranded adapter was added. Then 9 µL of ligation mix (1.11x T4 ligase reaction buffer, 4.44 mM ATP (NEB, P0756L), 2000 U T4 DNA ligase (NEB, M0202M)) was added to each sample, and the samples were incubated at 16°C for 16 hours. For H-M-Dyad-seq and H-H-Dyad-seq, 10 µL of AbaSI digestion mix (10 U AbaSI (NEB, R0665S), 1x CutSmart buffer) was added to each sample and the samples were incubated at 25°C for 2 hours, and then heated to 65°C for 20 minutes. Next, 1 µL of barcoded 1 µM double-stranded adapter was added. Then 9 µL of ligation mix (1.11x T4 ligase reaction buffer, 4.44 mM ATP (NEB, P0756L), 2000 U T4 DNA ligase (NEB, M0202M)) was added to each sample, and the samples were incubated at 16°C for 16 hours. After ligation, up to three barcoded libraries of the same type were pooled and all Dyad-seq versions were subjected to a 1x AMPure XP bead cleanup (Beckman Coulter, A63881), and eluted in 40 µL of water. M-M-Dyad-seq and H-M-Dyad-seq samples were then concentrated to a volume of 28 µL and subjected to nucleobase conversion using the NEBNext enzymatic methyl-seq conversion module (NEB, E7125S) according to the manufacturer’s recommendations except for performing the final elution step in 40 µL of water. For M-H-Dyad-seq and H-H-Dyad-seq samples, nucleobase conversion was performed using the NEBNext enzymatic methyl-seq conversion module similar to what has been described previously11. Briefly, samples were first concentrated to a volume of 17 µL. Then 4 µL of formamide (Sigma-Aldrich, F9037-100ML) was added and the samples were heated to 85°C for 10 minutes before being quenched on ice. APOBEC nucleobase conversion was performed as described by the manufacturer except for two minor changes. Samples were incubated at 37°C for 16 hours, and the final elution step was performed using 40 µL of water. To all Dyad-seq versions, the nucleobase converted samples were subjected to one round of linear amplification. To do this, 9 µL of amplification mix was added (5.56x NEBuffer 2.1 (NEB, B7202S), 2.22 mM dNTPs (NEB, N0447L), and 2.22 uM Linear amplification 9-mer: 5’- GCCTTGGCACCCGAGAATTCCANNNNNNNNN -3’) and the samples were heated to 95°C for 45 seconds before being quenched on ice. Once cold, 100 U of high concentration Klenow DNA polymerase (3’-5’ Exo-) (fisher scientific, 50-305-912) was added. Then samples were quickly vortexed, centrifuged and then incubated at 4°C for 5 minutes, followed by an increase of 1°C every 15 seconds at a ramp rate of 0.1°C per second till the samples reach 37°C which was then held for an additional 1.5 hours. Afterwards a 1.1x AMPure XP bead cleanup was performed, and the samplers were eluted in 40 µL of water before being concentrated down to 10 µL. The entire sample was then used in a linear PCR reaction by adding 15 µL of PCR mix (1.67x high-fidelity PCR mix (NEB, M0541L) and 0.67 µM Extended RPI primer: 5’- AATGATACGGCGACCACCGAGATCTACACGTTCAGAGTTCTACAGTCCGACGATCGGTGTAGTGGGTTTGG-3’) and performing PCR as follows: Initial denaturing at 98°C for 30 seconds, followed by 16 cycles of 98°C for 10 seconds, 59°C for 30 seconds, and 72°C for 30 seconds, and a final extension step at 72°C for 1 minute. Next, 5 µL of the linear PCR product was amplified further in a standard Illumina library PCR reaction, incorporating a uniquely indexed i7 primer. The remaining linear PCR product was stored at -20°C. To the final sequencing library, two 0.825x AMPure XP bead cleanups were performed with a final elution volume of 15 µL in water. The libraries were then quantified on an Agilent Bioanalyzer and Qubit fluorometer. Finally, libraries were subjected to paired-end 150 bp Illumina sequencing on a HiSeq platform.

treatment_protocol: Decitabine treatment: E14 mouse embryonic stem cells were cultured as described above. Upon passage of the E14 cells, SL media was supplemented with 0.05 µM of Decitabine. After 24 hours, cells were harvested using 0.25% trypsin-EDTA. The trypsin was then inactivated using serum containing medium. The cells were washed with 1x DPBS and then resuspended in 200 µL of DPBS. Genomic DNA was extracted using the DNeasy kit (Qiagen, 69504) according to the manufacturer’s recommendations. K562 cells were cultured as described above. Upon passage, the media was supplemented with 0.6 µM of Decitabine or DMSO vehicle control. After 24 hours the cells were washed and single-cell FACS sorting was performed as described above. Transition from serum to 2i and other media conditions: E14 mouse embryonic stem cells were cultured in SL conditions as described above. Upon passage, cells were resuspended in the following media depending on the condition studied. Commercial 2i media containing LIF (Millipore, SF016-200) was used for BL, G, 2i, and M experiments. For 2i, all components were used according to the manufacturer's recommendations. For G and M conditions, only the GSK3B inhibitor or MEK1/2 inhibitor was added, respectively. For the BL condition, no inhibitors were added. For the No condition, commercial 2i media without LIF (Millipore, SF002-100) was used with no inhibitors added. After 24 hours, the cells were washed with 1x DPBS and the media was exchanged. 48 hours after the initial media switch, the cells were collected using 0.25% trypsin-EDTA, quenched using serum containing media, washed in 1x DPBS and finally resuspended in 1x DPBS. The sample was then split in half for genomic DNA and total RNA extraction. In single-cell serum to 2i experiments, the same process was followed with cells being isolated into a reaction well of a 384 well plate using FACS after 3, 6, or 10 days in 2i. Cells grown in 2i were split 1:6 every other day.

value: N/A (Synthetic DNA Oligo)


title: Plastique_3

city: Montreal

first: Borhane

last: Annabi

state: Quebec

address: 2101 Jeanne-Mance

department: Chemistry

country: Canada

institute: Université du Québec à Montréal

data_processing:
Basecalls performed using Illumina RTA 2.4.11.
Samples demultiplexed using bcl2fastq 2.20 allowing 1 mismatch in the index.
Sequenced reads were trimmed for sequencing adapters and low quality extremities and mapped to the reference genome using STAR version 2.5.1b
Readcounts were computed by STAR during sequence alignment based on gene annotations from Gencode version M23 (based on Ensembl 98)
Expression values were also computed using RSEM version 1.2.28 based on Gencode version 37
Assembly: GRCh38
Supplementary files format and content: Readcounts: Tab-delimited file where columns are Ensembl gene identifier, counts for unstranded RNA, counts for 1st strand aligned, counts for 2nd strand aligned
Supplementary files format and content: RSEM: Tab-delimited file where columns correspond to a standard RSEM output for gene values (first line identifies the column)

organism: Homo sapiens

growth_protocol: Cells were plated on plastic (2D monolayers) in high-glucose alphaMEM supplemented with 10% FBS and 50 units/mL penicillin/streptomycin and cultured in a humidified incubator at 37°C with 5% CO2. MSC were kept subconfluent and expanded in number over 10 passages by a 1:2 split on a weekly basis.

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) + RNeasy mini kit (Qiagen, #74106)
cDNA libraries were prepared from total RNA using a PolyA selection and the KAPA RNA Hyperprep Kit and were further amplified for sequencing.

treatment_protocol:
VM was assessed in vitro using Cultrex (3432-010-01, R&D Systems) to monitor 3D capillary-like structures formation. In brief, each well of a 96-well plate was pre-coated with 50 μl of Cultrex. MSC suspension in culture media (104 cells/100 μl) was then seeded on top of polymerized Cultrex for 6 hours.
RGCG treatment was performed on 2D cell monolayers in the presence of 30 uM EGCG in serum free media for 24 hours.

value: Mesenchymal stem cells

value: Wt

value: 2D cell monolayers


title: Plastique_2


title: Cultrex_2

value: 3D differentiation on Cultrex


title: Cultrex_1


title: C_EGCG_2

value: EGCG 30 microM, 24 hours


title: C_EGCG_3


title: C_EGCG_1


title: OCIAML2.shFBL.H3K9me3

city: Stuttgart

first: Haiyang

last: Yun

address: Auerbachstraße 112

country: Germany

institute: Robert Bosch Center for Tumor Diseases

data_processing:
The sequencing reads were aligned to the human reference genome (hg38) using Bowtie and subject to QC check.
Repeat reads were removed using PICARD tools.
bigwig files were generated from uniquely mapped reads of each sample and were normalised to library size (as counts per million, CPM) by running bamCoverage from deepTools.
Peaks were called using MACS2 with a P value cutoff of 1 × 10^-9 and with setting ‘nomodel’.
Assembly: hg38
Supplementary files format and content: Normalised (CPM) bigwig files for visualisation

source_name: peripheral blood

growth_protocol: Cells were cultured in Gibco RPMI 1640 medium (with L-Glutamine) containing 10% fetal bovine serum and 1% Penicillin- Streptomycin.

extract_protocol:
ChIP was performed using an Diagenode iDeal ChIP-seq kit for H3K27ac, H3K9me3, and FBL following the manufacturer’s recommendations. Briefly, one or five million cells per IP condition were crosslinked with formaldehyde at a final concentration of 1% for 10 min and then quenched by addition of Glycine. Cells were then lysed to harvest nuclei. Chromatin was sheared using the Diagenode Bioruptor for 20 cycles. Subsequently, immunoprecipitation, washing, decrosslinking and DNA elution was performed stepwise to harvest the ChIPed DNA.
Immunoprecipitated DNA was processed for library preparation using NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs), following standard procedures from manufacturer. The library DNA was quantified using Qubit and library average size was determined by Agilent DNA 1000 Kit (Agilent Technologies).

treatment_protocol: Cells were transduced with lentiviral shRNA control or targeting Fibrillarin.

value: peripheral blood

value: acute myeloid leukemia

value: transduced with lentiviral shRNA targeting FBL

tag: chip antibody


title: OCIAML2.shFBL.H3K27ac

value: H3K27ac (Abcam, #ab4729)


title: OCIAML2.shCtrl.H3K9me3

value: transduced with lentiviral shRNA control


title: OCIAML2.shFBL.FBL

value: FBL (Abcam, #ab5821)


title: ATAC-seq_WT_BM1_IL18Ra+ST2-PD1+IL17RB-


title: OCIAML2.shCtrl.FBL


title: MV411.shFBL.H3K9me3


title: ATAC-seq_ILC2_steady_state

data_processing:
ATAC-seq data were aligned to mm10 genome assembly using Bowtie2 with single-end mode. Mapped fragments were trimmed 4 bp from the start and 5 bp from the end using bedtools. The data were visualized and the peaks were identified using the HOMER package.
Assembly: mm10
Supplementary files format and content: bedgraph

source_name: Lung

extract_protocol:
Lungs were cut into small pieces and digested in RPMI containing collagenase A and Dnase I using gentleMACS Dissociator and then passed through 70 µm filter. Lung ILC2s were sorted by SONY SH800.
ATAC-seq library was generated using Omni-ATAC protocol.

tag: strain

value: Lung


title: T2-450-3

city: İstanbul

first: Tugba

last: Bagci-Onder

address: Rumelifeneri Yolu, Sarıyer

department: Koç University Research Center for Translational Medicine

country: Turkey

institute: Koç University

description:
T2-450-3 column of tpm_counts.txt
tpm_counts.txt
DEG_T2-450.txt

data_processing:
Reads were trimmed using trimmomatic, pseaudoaligned using kallisto with an index built from the hg38 cDNA fasta reference sequence, and then quality of the pseudoalignment was assessed using FastQC. Differential gene expression was performed using the DESEq2 package. For parental-resistant comparisons, differentially expressed genes (DEGs) were defined with a threshold for Log2FoldChange>2 (up-regulated) or Log2FoldChange<-2 (down-regulated) and p<0.001. For drug or sgRNA treated T1-160 cells, DEGs were determined as the genes that have padj<0.05. Gene set enrichment analysis was performed with Log2FoldChange rank-ordered gene lists by using GSEA software and all available gene sets from MsigDB at the date of January 24th, 2022 [35].
Assembly: hg38
Supplementary files format and content: tpm_counts files contain normalized count (transcript per million) data for each replicate of parental and resistant cells.
Supplementary files format and content: DEG files contain log2foldchanges, pvalue and FDR values for each gene.

growth_protocol: SUM159PT cells were cultured in Ham’s F12 nutrient mix (Gibco, USA) supplemented with 5% FBS, 5 μg/ml insulin (Sigma-Aldrich, USA), 1 μg/ml hydrocortisone (Sigma-Aldrich, USA) and 10 mM HEPES (Thermo Fisher, USA). Cells were maintained in a humidified incubator at 37oC with 5% CO2 level.

extract_protocol:
Total RNAs were isolated by using MN Nucleospin RNA isolation kit according to manufacturer’s instructions.
Library preparation and sequencing of parental versus resistant cell RNA samples were performed at BGI (Hong Kong) according to company's library preparation protocol for BGIseq500. Samples were sequenced as single end. Library preparation and RNA sequencing of inhibitor or gRNA treated T1-160 cells were perfomed at University of Oxford (Oxford, UK). Briefly, RNA was DNase I treated,cleaned and concentrated (Zymo RNA Clean and Concentrator, Zymo Research) then enriched for poly(A) mRNA (NEBNext poly(A) mRNA Magnetic Isolation Module, NEB Biosystems, Ipswich, UK). Sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep kit (New England Biolabs). RNA quality was assessed using High Sensitivity RNA Screentape and an Agilent 4200 tapestation. Single-indexed and multiplexed samples were run on an Illumina Next Seq 500 sequencer using a NextSeq 500 v2 kit (FC-404–2005; Illumina, Can Diago, CA) for paired-end sequencing.

treatment_protocol: Cells were seeded as 2x105 cells/well in 6- well plates. Next day, they were treated with either IC10 (0.4 nM) or IC50 (1.5 nM) values of Taxol for 3 days as starting concentrations. When cells became confluent under drug treatment, concentrations were doubled. If cells did not look healthy or were too sparse, they were taken into drug-free medium until they form colonies. Upon reaching confluence, last concentration of drug was applied again, and the procedure was repeated. Alongside, DMSOtreated. parental cell lines were aged as controls. Drug treatment was continued until significant difference between IC50 values of parental and resistant cell lines was obtained. Resistant cells derived from SUM159PT cells were named according to the initial and final doses of Taxol applied. Cells were maintained in the final dose of Taxol (160 nM for T1-160 and 450 nM for T2-450) while culturing.

value: Taxol-resistant Invasive Breast Carcinoma

value: Taxol-resistant


title: T2-450-2

description:
T2-450-2 column of tpm_counts.txt
tpm_counts.txt
DEG_T2-450.txt

value: WT


title: OCIAML2.shCtrl.H3K27ac


title: MV411.shFBL.H3K27ac


title: MV411.shFBL.FBL


title: MV411.shCtrl.H3K9me3


title: MV411.shCtrl.H3K27ac


title: T2-450-1

description:
T2-450-1 column of tpm_counts.txt
tpm_counts.txt
DEG_T2-450.txt


title: T1-160-3

description:
T1-160-3 column of tpm_counts.txt
tpm_counts.txt
DEG_T1-160.txt


title: T1-160-1

description:
T1-160-1 column of tpm_counts.txt
tpm_counts.txt
DEG_T1-160.txt


title: Plastique_1

value: Bone marrow


title: MV411.shCtrl.FBL


title: Cultrex_3


title: Parental-2

description:
Parental-2 column of tpm_counts.txt
tpm_counts.txt

value: Invasive Breast Carcinoma


title: Kasumi1.shFBL.H3K27ac


title: Kasumi1.shFBL.FBL


title: Kasumi1.shFBL.H3K9me3


title: Parental-1

description:
Parental-1 column of tpm_counts.txt
tpm_counts.txt


title: Parental-3

description:
Parental-3 column of tpm_counts.txt
tpm_counts.txt


title: Kasumi1.shCtrl.H3K27ac


title: SF370_DCRISPR-Cas_stat_biolrep3

city: Baltimore

first: Joshua

last: Modell

state: MD

address: 725 N Wolfe St, PCTB 614

institute: Johns Hopkins University School of Medicine

data_processing:
Transcripts were quantified with Salmon (v1.8.0)
Assembly: AE004092
Supplementary files format and content: Tab-delimited file containing feature length, TPM, and total reads for each gene feature

organism: Streptococcus pyogenes

extract_protocol:
After cell lysis, RNA was extracted with the Direct-zol™ RNA Miniprep Kit (Zymo Research) and treated with Promega RQ1 DNase (M6101) to digest contaminating DNA.
Multiplexed libraries were prepared with NEBNext® rRNA Depletion Kit (Bacteria) (E7850L) and NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (E7760S) using 450 ng total RNA input. PCR amplification was performed for 11 rounds with NEBNext® Multiplex Oligos for Illumina®.

value: {delta}CRISPR-Cas

tag: growth phase

value: stationary

value: rRNA-depleted total RNA


title: SF370_DCRISPR-Cas_stat_biolrep1


title: Kasumi1.shCtrl.H3K9me3


title: Kasumi1.shCtrl.FBL


title: MV411_iMARGI_e4

data_processing:
Sequencing data were aligned to the hg38 reference genome using STAR (v2.5.4b).
In-house scripts were used to deduplicate (FastUniq v1.1) and parse (Samtools v1.6) the mapped read pairs to obtain the BEDPE file with the uniquely mapped read pairs.
Assembly: hg38
Supplementary files format and content: Annotated RNA-DNA interaction pairs
Library strategy: iMARGI

extract_protocol:
Ten million of MV4-11 cells were harvested from culture and were crosslinked using 1% formaldehyde at room temperature for 10 minutes and quenched with glycine. Cells were lysed for nuclei isolation, followed by RNA and DNA fragmentation in the nuclei using RNase I and restriction enzyme AluI. Subsequently, a RNA/DNA hybrid linker was ligated to the fragmented RNA and then to the DNA with spatial proximity. This was followed by crosslinking reversal, nucleic acids isolation, and unligated linkers removal. Magnetic streptavidin beads were utilized to further pull down the RNA- linker-DNA ligation fragments. The RNA elements were reverse transcribed into cDNA, and the new double stranded fragments were heat denatured to release the single strand containing DNA-linker-cDNA. This single stranded DNA-linker-cDNA was further subject to circularization, oligo annealing to form a BamHI site, re-linearization by BamHI digestion. As the linearized DNA contained 5’ and 3’ sequences compatible with Illumina sequencing, samples were amplified with PCR and size-selected for pair-end sequencing (2 x 75bp) on Illumina NextSeq.
Library was generated using custom primers through PCR amplification step in the iMARGI protocol


title: SF370_DCRISPR-Cas_log_biolrep3

value: logarithmic


title: T1-160-2

description:
T1-160-2 column of tpm_counts.txt
tpm_counts.txt
DEG_T1-160.txt


title: MV411_U8_ChIRP

data_processing:
The sequencing reads were aligned to the human reference genome (hg38) using Bowtie and subject to QC check.
Repeat reads were removed using PICARD tools.
bigwig files were generated from uniquely mapped reads of each sample and were normalised to library size (as counts per million, CPM) by running bamCoverage from deepTools.
Assembly: hg38
Supplementary files format and content: Normalised (CPM) bigwig files for visualisation
Library strategy: ChIRP

extract_protocol:
20~30 million MV4-11 cells were collected per ChIRP condition. Crosslinking was executed with 1% glutaraldehyde for 10 minutes at room temperature and quenched by addition of glycine. Cells were then lysed and lysate was sonicated using a Bioruptor Standard (Diagenode), with a setting of 30 seconds ‘ON’ and 45 seconds ‘OFF’ pulse intervals for 1~1.5 hours in a 4 °C water bath, till lysate turned clear. Next, biotinylated DNA probes (for control, U1, U3/SNORD3A, or U8/SNORD118) were added to hybridize with individual target RNA. RNA-associated chromatin was subsequently captured using magnetic dynabeads and underwent thorough washes. Afterwards, crosslinking reversal was performed and DNA was isolated.
The DNA elute was subject to NGS library preparation using NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs). The library was individually barcoded and pooled to load onto Illumina NextSeq for single-read sequencing (1 x 50 bp).

tag: chirp probe

value: targeting U8 snRNA (5'-GGATTATCCCACCTGACGAT/3BioTEG/-3')


title: SF370_DCRISPR-Cas_log_biolrep1


title: MV411_iMARGI_e1

value: peripheral blood


title: 5448_stat_ChIP

data_processing:
Reads were trimmed with TrimGalore (0.6.10) using a Q score cutoff of 30
Reads were aligned to the reference genome with bwa mem (bwa version 0.7.17-r1188)
Peaks were called with MACS2 version 2.2.7.1
Bigwig files of reads per million were made with deeptools using a bin size of 20bp (bamCoverage command from deeptools version 3.5.0)
Assembly: AE004092 (SF370) and CP008776 (5448)
Supplementary files format and content: bigwig, narrowPeak

extract_protocol:
Cells were fixed with 1% formaldehyde for 20 min. After quenching and cell lysis, sonication was performed with a Branson Sonifier 450.
Cas9 IP and input control libraries were prepared with the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® and NEBNext® Multiplex Oligos for Illumina®. 1 ng DNA was used as input and 9 cycles were used for PCR amplification.

value: Cell Signaling Technology Cas9 (7A9-3A3) Mouse mAb #14697


title: SF370_DCRISPR-Cas_log_biolrep2


title: 5448_stat_input


title: MV411_iMARGI_e2

value: acute myeloid leukemia


title: 5448_log_input


title: MV411_U1_ChIRP

value: targeting U1 snRNA (5'-CTCCCCTGCCAGGTAAGTAT-3')


title: SF370_DCRISPR-Cas_stat_biolrep2


title: MV411_CTRL_ChIRP


title: MV411_iMARGI_e3


title: SF370_DtrL_stat_biolrep2

value: {delta}tracr-L


title: MV411_shSNORD118_ATAC_e2

data_processing:
The sequencing reads were aligned to the human reference genome (hg38) using Bowtie and subject to QC check.
Repeat reads were removed using PICARD tools.
bigwig files were generated from uniquely mapped reads of each sample and were normalised to library size (as counts per million, CPM) by running bamCoverage from deepTools.
Assembly: hg38
Supplementary files format and content: Normalised (CPM) bigwig files for visualisation

extract_protocol:
ATAC-seq was carried out using an ATAC-seq kit from Active Motif following manufacturer's instruction. In brief, 100,000 freshly isolated cells were pelleted and washed with ice-cold PBS. The cell pellet was collected and was resuspended in Lysis buffer. The crude nuclei pellet was preserved for tagmentation using ATAC-seq kit (Active Motif) for 30 minutes incubation at 37 °C. Afterwards, transposed DNA was purified using with MinElute PCR Purification kit (Qiagen).
Eluted DNA was amplified by setting the PCR cycling as below: step 1. 72 °C 5 minutes, 98 °C 30 seconds; step 2. 10 cycles: 98 °C 10 seconds, 63 °C 30 seconds, and 72 °C 1 minute; step 3. 72 °C 5 minutes. PCR products were again purified with Qiagen MinElute PCR Purification kit. The quantity and quality of library DNA was measured using Qubit and and Bioanalyzer 2100 system with a High Sensitivity DNA chip (Agilent Technologies). The pooled libraries were sequenced for paired-read (2 × 75 bp) sequencing on an Illumina NextSeq at the EMBL Genecore Genomics Facility. Two biological replicates were performed independently for each treatment.

treatment_protocol: Cells were transduced with lentiviral shRNA control or targeting SNORD118.

value: transduced with lentiviral shRNA targeting SNORD118


title: SF370dtrL_stat_input


title: 5448_log_ChIP


title: MV411_shSNORD118_ATAC_e1


title: SF370_DtrL_stat_biolrep1


title: SF370dtrL_log_input


title: SF370dtrL_stat_ChIP


title: MV411_shCTRL_ATAC_e2

value: transduced with lentiviral shRNA control


title: SF370_DtrL_stat_biolrep3


title: H7

city: chengdu

first: tong

last: feng

state: -- None selected --

address: Acupuncture and Tuina College

institute: Chengdu University of TCM

data_processing:
Raw sequencing data underwent the quality control process to assess the data usability. Then data was pre-processed to produce the trimmed data aligned with the reference genome (STAR version 2.5.2b). MiRNAs were included in the statistical analysis when the mean of counts per million reads ≥ 1. Differential expressions of miRNAs were calculated with the edgeR package (version 3.20.9) in the statistical R program (version 3.5.0).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: serum

extract_protocol:
total RNA extracted from purified exosomes was examined using agarose electrophoresis and quantified using nanodrop, respectively.
MiRNA library was constructed with NEB Multiplex Small RNA Library Prep Set for Illumina (Illumina, USA) based on the manufacturer’s instructions. The quality of sequencing libraries was tested with Agilent 2100 Bioanalyzer. Libraries were mixed and degenerated into single-stranded DNA with 0.1M NaOH. The mixed samples were sequenced 50 cycles with Illumina NextSeq 500 (Illumina, USA).

value: serum


title: MV411_shCTRL_ATAC_e1


title: SF370_DtrL_log_biolrep3


title: SF370_DtrL_log_biolrep2


title: H34


title: H33


title: SF370dtrL_log_ChIP


title: H31


title: H27


title: H26


title: MV411_U3_ChIRP

value: targeting U3 snRNA (5'-TTCGGTGCTCTACACGTTCA/3BioTEG/-3')


title: SF370_DtrL_log_biolrep1


title: H25


title: SF370_stat_biolrep3

value: WT


title: SF370_stat_ChIP


title: H24


title: SF370_stat_biolrep2


title: SF370_log_input


title: H21


title: H20


title: SF370_stat_biolrep1


title: 6


title: SF370_log_ChIP


title: 30


title: 3


title: SF370_log_biolrep2


title: pancreatic rat islets, LP_4, 22-day-old

city: Lausanne

first: Cecile

last: Jacovetti

address: Rue du Bugnon 9

department: Fundamental Neurosciences

country: Switzerland

institute: University of Lausanne

data_processing:
Sequencing quality was examined by FastQC software and trimmed reads were aligned to mouse and rat mature-tRNA and pre-tRNA sequences from GtRNAdb.
For small RNA sequencing, the sequencing type was 50-bp single-read at 145 M reads.
Unique sequences (considering UMI codes) were counted.
We set the minimum cpm value as at least 5 reads in the smallest library. Only sequences above the minimum cpm value in at least 3 samples were retained.
The remaining reads were aligned to the transcriptome sequences (miRNA, piRNA, rRNA, snRNA, snoRNA).
Assembly: UCSC (http://gtrnadb.ucsc.edu/GtRNAdb2/genomes/eukaryota/Rnorv6/Rnorv6-seq.html)
Supplementary files format and content: tab-delimited text file includes raw counts (reads) for each sample.
Supplementary files format and content: tab-delimited text file includes normalized counts for each sample.
Supplementary files format and content: tab-delimited text file includes tRF sequences and host tRNAs.
Supplementary files format and content: tab-delimited text file includes fold-change and adjusted p values for each sample (cut-off adjusted P ≤ 0.05, FC > 2).

organism: Rattus norvegicus

source_name: pancreatic islets

growth_protocol: Rat pancreatic islets were isolated by collagenase digestion followed by Histopaque density gradient and handpicking.

extract_protocol:
Total RNA from rat islets was extracted using miRNeasy micro kit (Qiagen # 217084).
Nucleotide modifications were removed from RNA samples prior to sequencing library construction by the following treatments using the rtStar™ tRF&tiRNA Pretreatment kit (Arraystar # AS-FS-005): 3’-aminoacyl (charged) deacylation to 3’-OH for 3’ adaptor ligation, 3’-cP (2’,3’-cyclic phosphate) removal to 3’-OH for 3’ adaptor ligation, 5’-OH (hydroxyl group) phosphorylation to 5’-P for 5’ adaptor ligation, and N1-methyladenosine (m1A), 3-methylcytidine (m3C) and 1-methyl guanosine (m1G) demethylation. 10 ng of total RNA was used for the construction of sequencing cDNA libraries using QIAseq miRNA NGS 48 Index IL kit (Qiagen # 331595) following manufacturers's protocol.

value: pancreatic islets

value: Srague Dawley

value: low-protein diet (5.3 % protein, 17 % carbohydrate, 77.7 % fat (Safe diet, France (U8959P Version 0156))


title: pancreatic rat islets, LP_3, 22-day-old


title: 27


title: 23


title: SF370_log_biolrep1


title: pancreatic rat islets, LP_2, 22-day-old


title: SF370_stat_input

value: stationary


title: 22


title: 25


title: B cells WT #3

city: Quebec

first: Reda

last: Fazazi

state: Qc

address: 2705 blvd Laurier

institute: Laval University

data_processing:
Paired-end mRNAseq fastq datasets were trimmed with trimmomatic v0.39. Trimmed fastq files were mapped on the M. musculus or H. sapiens genome (Ensemble; Mus_musculus.GRCm39.cds.all.fa.idx) and quantified using kallisto 0.44.0.
Assembly: Ensemble; Mus_musculus.GRCm39.cds.all.fa.idx
Supplementary files format and content: Both files countain for each samples the normalized counts directly generated by kallisto four each gene.

source_name: Central nervous system

extract_protocol:
At experimental endpoints, CNS tissues from WT and IgH[MOG] mice were necropsied and mononuclear cells were isolated. Live CD19+ B cells and CD4+PD1+CXCR5- Tph cells were purified by high-speed sorting (FACSAria II) and were directly processed using NEBNext Single Cell/Low Input RNA Library Prep Kit (New England Biolabs), according to the manufacturer’s instructions, for mRNA sequencing library preparation.
Total mRNA was enriched using poly(A)+ primers and template-switching oligo synthesize double-stranded cDNA with reverse transcriptase. A PCR amplification of 21 cycles was performed to increase cDNA yields followed by a purification step with AxyPrep Mag PCR Clean-up kit (Axygen, Big Flats, NY, USA). Enzymatic fragmentation of cDNA and end-repair steps were followed by ligation of NEBNext adaptors and PCR enrichment step of 11 cycles to incorporate specific indexed adapters for the multiplexing. The quality of final amplified libraries was examined with a DNA screentape D1000 on a TapeStation 2200 and the quantification was done on the QuBit 3.0 fluorometer (ThermoFisher Scientific, Canada). Subsequently, mRNA-seq libraries with unique dual indexes were pooled together in equimolar ratio and sequenced for paired-end 100 pb sequencing on NovaSeq 6000 at the Next-Generation Sequencing Platform, Genomics Center, CHU de Québec-Université Laval Research Center. The average insert size for the libraries was 253 bp. The mean coverage/sample was 24M paired-end reads.

value: Central nervous system

value: B220+ B cell

value: NOD (WT)


title: pancreatic rat islets, LP_1, 22-day-old


title: 21


title: 20


title: 26


title: pancreatic rat islets, CD_5, 22-day-old

value: chow diet (16.8 % protein, 17.4% carbohydrate, 65.8 % fat (U8978P Version 0022))


title: B cells WT #2


title: 2


title: B cells WT #1


title: 19


title: 18


title: B cells IgH[MOG] #3

value: IgH[MOG]


title: SF370_log_biolrep3

value: logarithmic

value: rRNA-depleted total RNA


title: 29


title: 15


title: T1-160_BRPF1_g3-3

description:
g3-3 column of tpm_BRPFinh_and_KO.txt
tpm_BRPFinh_and_KO.txt
DEG_NT1vsg3.txt

value: Taxol-resistant Invasive Breast Carcinoma

value: BRPF1 Knockout

value: BRPF1 sgRNA #3

tag: time

value: Day 12


title: pancreatic rat islets, CD_4, 22-day-old


title: pancreatic rat islets, CD_2, 22-day-old


title: T1-160_BRPF1_g3-2

description:
g3-2 column of tpm_BRPFinh_and_KO.txt
tpm_BRPFinh_and_KO.txt
DEG_NT1vsg3.txt


title: B cells IgH[MOG] #2


title: pancreatic rat islets, CD_1, 22-day-old


title: T1-160_BRPF1_g2-2

description:
g2-2 column of tpm_BRPFinh_and_KO.txt
tpm_BRPFinh_and_KO.txt
DEG_NT1vsg2.txt

value: BRPF1 sgRNA #2


title: T1-160_BRPF1_g2-1

description:
g2-1 column of tpm_BRPFinh_and_KO.txt
tpm_BRPFinh_and_KO.txt
DEG_NT1vsg2.txt


title: B cells IgH[MOG] #1


title: T1-160_NT1-3

description:
NT3 column of tpm_BRPFinh_and_KO.txt
tpm_BRPFinh_and_KO.txt

value: WT

value: Non-targeting sgRNA


title: IDD 5

city: Pok Fu Lam

first: Peikai

last: Chen

address: Sassoon Road 5

department: Faculty of Medicine

country: Hong Kong

institute: The University of Hong Kong

description: degenerated and aged

data_processing:
The fastq read-pairs were aligned to human reference genome using the HISAT2 aligner
The resulting SAM files were sorted and re-formatted as BAM files using SAMTOOLS (0.1.18)
The BAM files were quantified to human gene model by GENCODE (v25) using Cufflinks and HTSeq-count
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM and COUNT values for each Sample for all genes

source_name: nucleus pulposus

extract_protocol:
RNA extraction from dissociated cells was done by using Ambiion RNA extraction kit (CAT#AM-1560). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol:
None
None

value: nucleus pulposus

tag: ivd level

tag: condition

value: L3-L5 degenerative-slip & stenosis, degenerative spondylolisthesis

tag: gender

value: M

tag: age

tag: schneiderman

tag: pfirrmann


title: Tph cells WT #2

tag: tissue

value: Central nervous system


title: Tph cells WT #3


title: T1-160_NT1-1

description:
NT1 column of tpm_BRPFinh_and_KO.txt
tpm_BRPFinh_and_KO.txt

tag: cell line

tag: treatment


title: T1-160_NT1-2

description:
NT2 column of tpm_BRPFinh_and_KO.txt
tpm_BRPFinh_and_KO.txt

tag: cell type


title: IDD 4

description: degenerated and aged

value: L2-3,L4-5 stenosis & spinal claudication


title: T1-160_OF-1-2

description:
of2 column of tpm_BRPFinh_and_KO.txt
tpm_BRPFinh_and_KO.txt
DEG_DMSOvsOF-1.txt

tag: genotype

value: 72 hours


title: IDD 3

description: degenerated and aged

value: L5-S1 degenerative spondylolisthesis


title: pancreatic rat islets, CD_3, 22-day-old

value: pancreatic islets

value: Srague Dawley

value: chow diet (16.8 % protein, 17.4% carbohydrate, 65.8 % fat (U8978P Version 0022))


title: Tph cells IgH[MOG] #3

value: IgH[MOG]


title: T1-160_BRPF1_g2-3

description:
g2-3 column of tpm_BRPFinh_and_KO.txt
tpm_BRPFinh_and_KO.txt
DEG_NT1vsg2.txt

value: Taxol-resistant Invasive Breast Carcinoma

value: BRPF1 Knockout


title: IDD 2

description: degenerated

value: L4-5 disc degeneration with disc herniation


title: T1-160_PFI-4-3

description:
pf3 column of tpm_BRPFinh_and_KO.txt
tpm_BRPFinh_and_KO.txt
DEG_DMSOvsPFI-4.txt

value: PFI-4 (5µM)


title: T1-160_PFI-4-2

description:
pf2 column of tpm_BRPFinh_and_KO.txt
tpm_BRPFinh_and_KO.txt
DEG_DMSOvsPFI-4.txt

value: WT


title: T1-160_PFI-4-1

description:
pf1 column of tpm_BRPFinh_and_KO.txt
tpm_BRPFinh_and_KO.txt
DEG_DMSOvsPFI-4.txt


title: IDD 1

description: degenerated

value: F


title: T1-160_BRPF1_g3-1

description:
g3-1 column of tpm_BRPFinh_and_KO.txt
tpm_BRPFinh_and_KO.txt
DEG_NT1vsg3.txt

value: BRPF1 sgRNA #3

value: Day 12


title: Tph cells IgH[MOG] #2


title: T1-160_OF-1-3

description:
of3 column of tpm_BRPFinh_and_KO.txt
tpm_BRPFinh_and_KO.txt
DEG_DMSOvsOF-1.txt


title: T1-160_OF-1-1

description:
of1 column of tpm_BRPFinh_and_KO.txt
tpm_BRPFinh_and_KO.txt
DEG_DMSOvsOF-1.txt


title: T1-160_DMSO-2

description:
dmso2 column of tpm_BRPFinh_and_KO.txt
tpm_BRPFinh_and_KO.txt

value: DMSO


title: T1-160_DMSO-1

description:
dmso1 column of tpm_BRPFinh_and_KO.txt
tpm_BRPFinh_and_KO.txt


title: SI-HSPA2-3

city: Jinan

first: jiayin

last: Gao

state: --- Select One ---

address: Center for Reproductive Medicine, Shandong University, Jinan, Shandong 250012, C

institute: shandong university

data_processing:
fastqc Checking SEQUENCING quality
hisat2, samtools mapping to the genome
featureCounts count bam files.Get the expression matrix
Assembly: mm39
Supplementary files format and content: processed data.txt

source_name: embryo

extract_protocol:
Total RNA extracted purified with Discover-scTM WTA Kit V2 (N711, Vazyme), according to the manufacturer's instructions
Sequencing libraries were generated using TruePep™DNA Library Prep Kit V2 for Illumina® (TD502, Vazyme) according to manufacturer’s recommendations. The libraries were performed on an Illumina Hiseq X-ten platform with 150 bp paired-end.

value: embryo

tag: strain background

value: ICR

value: HSPA2 Knockdown


title: T1-160_DMSO-3

description:
dmso3 column of tpm_BRPFinh_and_KO.txt
tpm_BRPFinh_and_KO.txt

value: 72 hours


title: Tph cells WT #1

value: Central nervous system

value: NOD (WT)


title: SI-HSPA2-2


title: TERT

city: Houston

first: Hong Seok

last: Shim

state: TX

institute: MD Anderson Cancer Center

data_processing:
NextSeq RTA (version 2.4.11.0) was used for base calling. bcl2fastq (version 2.20.0) was used to convert the .bcl files into .fastq files. Fastq files were aligned to the human reference genome (hg19) using Bowtie. SAMtools was used to convert .sam file to .bam file. Deeptools was used to generate .bigwig files. Peaks were called using MACS version 1.4.
Assembly: hg19
Supplementary files format and content: bigwig

source_name: human iPSC-derived neurons

growth_protocol: Differentiated neurons were cultured in neural differentiation media (DMEM/F12, 1x GlutaMax, 1x N2, 1x B27 (Invitrogen), 20 ng/ml BDNF, 20 ng/ml GDNF (Peprotech), 1 µM dibutyryl-cyclic AMP, and 0.2 µM ascorbic acid (Sigma).

extract_protocol:
Cell lysates were clarified from sonicated nuclei and histone/TF-DNA complexes were isolated with antibody.
The ChIP-seq library was prepared using KAPA HyperPrep Kit (Roche) following manufacturer’s protocol

treatment_protocol: Human iPSCs were treated with DMSO or TAC.

value: human iPSC-derived neurons

value: differentiated neurons

tag: chip antibody

value: anti-TERT (Abcam, Cat#ab32020)


title: wildtype OP50 rep2

city: Kobe

first: Masaharu

last: Uno

address: 2-2-3, Minatojima-minamimachi, Chuo-ku

department: BDR

institute: RIKEN

data_processing:
fastqc 0.11.8
catadapt 2.7
trim_galore 0.6.4_dev
hisat2 2.1.0
samtools 1.7
stringtie 2.1.1
Assembly: WBcel235
Supplementary files format and content: csv file contains CPM values for each sample

organism: Caenorhabditis elegans

source_name: entire body

growth_protocol: Total RNA was isolated using TRIzol reagent (Invitrogen) from C. elegans Bristol strain N2 cultured in S basal medium with E. coli OP50 or L. paracasei subsp. paracasei 2004 for three days from three days after hatching.

extract_protocol:
Total RNAs were collected with TRIzol following manufacture's protocol.
RNA-seq library preparation and RNA sequencing were performed at Macrogen Inc. using Illumina HiSeq 2000 platform.

treatment_protocol: The animals were transferred to S-basal medium with OP50 or L. paracasei subsp. paracasei 2004 for 3day.

value: entire body

tag: strain

value: Bristol strain N2

value: wildtype

value: S basal medium with E. coli OP50


title: wildtype 2004 rep2

value: S basal medium with L. paracasei subsp. paracasei 2004


title: Tph cells IgH[MOG] #1

value: IgH[MOG]


title: TAC-treated H3K9me3

source_name: human MRC5 fibroblasts

growth_protocol: Fibroblasts were cultured in EMEM with 10% Fetal Bovine Serum (FBS), 1X penicillin/streptomycin (Invitrogen).

treatment_protocol: Fibroblasts were treated with DMSO or TAC.

value: human MRC5 fibroblasts

value: primary fibroblasts

value: anti-H3K9me3 (Abcam, Cat#ab8898)


title: DMSO-treated H3K9me3


title: wildtype 2004 rep1


title: SI-HSPA2-1

value: embryo

value: ICR


title: wildtype OP50 rep1


title: NC-3

value: WT

value: NC-FAM


title: TAC-treated H3K27ac

value: anti-H3K27ac (Abcam, Cat#ab4729)


title: GLI1+ cells from hypoxic mouse lungs

city: Giessen

first: Marek

last: Bartkuhn

state: Hessen

address: Aulweg 132

department: Biomedical Informatics and Systems Medicine

institute: Justus-Liebig-University Giessen

description: 10x Genomics scRNA-seq

library_source: transcriptomic single cell

data_processing:
Reads were processed using the Cell Ranger 2.1.0 pipeline with default and recommended parameters.
Unsupervised clustering and differential gene analyses were performed using the Seurat package.
Assembly: mm10
Supplementary files format and content: CellRanger outputs (count matrix, genes, barcodes) as .gz

source_name: lung

extract_protocol:
Fresh isolated mouse lung samples were flushed with HBSS and then cut into small pieces and filtered two times with 70um and 40um filters. GLI1+ cells are lineage labeled cells with red fluorescent, we first use CD31, CD45 and Epcam to eliminate non-mesenchymal cells. Then PE is used to select RFP+ GLI1+ cell for the single cell analysis.
Library sample index sequences were incorporated as the sample index read and sequenced together on a Nextseq2000 sequencer. Raw reads were aligned against the mouse genome (mm10, ensemble assembly 104) and mapped and counted by StarSolo.

value: lung

value: TdTomato positive mesenchymal lung cells from Gli1Cre-ERT2 mice

value: Hypoxia


title: NC-2

value: NV-FAM


title: DMSO-treated H3K27ac


title: PEAT_45FR

city: Umeå

first: Stephan

last: Wenkel

address: Parallellvägen 21

country: Sweden

institute: Umeå Plant Science Center

data_processing:
FastQC, Cutadapt, HISAT2 (v2.0.5), samtools, bedools,  hmmer3 and R
generic Illumina adapters were removed with Cutadapt . Additionally, Cutadapt removed PEAT-adapters and marked read direction for later identification of the RNA start.
HISAT2 (v2.0.5) aligned the reads with more than 90% success to the Arabidopsis thaliana TAIR9 genome assembly. Samtools (v0.1.19)  and bedtools (v2.17.0) filtered for properly paired reads with high aligment score (-q 10) and performed file conversions.
For each gene in TAIR10 annotation with at least 100 reads that indicate a transcription start site, TSS-reads were counted in sliding windows of 100 bp size and 50 bp steps, beginning 50 bp before the annotated gene start. Windows that had >= 10% of the total number of TSS-reads in that gene were fused when overlapping or directly touching and considered transcription start sites (TSS). Only genes with TSS in 5’UTR and at least one alternative TSS in coding sequence or intron were further analyzed.
Pfam-A domains were searched in protein sequences with hmmer3 and cutoffs of e-value <= 0.1 and c-value <= 0.05. Interaction domains were identified using iPfam.
Assembly: TAIR10
Supplementary files format and content: A text (.txt) space separated file containing genome coordinates of the analysed peaks, the corresponding genes and assigned protein domain, for all samples

organism: Arabidopsis thaliana

source_name: Whole 10 days old seedlings

extract_protocol:
Total RNA was extracted using either the Spectrum Plant Total RNA Kit (Sigma)
PEAT library preparation was done exactly as described in Ni et al., Paired-end analysis of transcriptional start sites, Protocol Exchange  (2010, doi:10.1038/nprot.2010.55), but all steps beginning with the circularization of the PCR product were omitted and the fragments were inserted into NEBNext Ultra™ II DNA Library Prep Kit for Illumina and quantified with NEBNext Library Quant Kit for Illumina. The finished libraries had a fragment size of 500 bp.

value: Whole 10 days old seedlings

value: Wild-type seedlings

value: 45 minutes FR enriched light


title: DKO_d0_medip

city: Toyonaka

first: Takamasa

last: Ito

state: Osaka

address: 1-1 Machikaneyama

department: Biological Science

institute: Osaka University

data_processing:
Raw sequence reads were trimmed using Trim Galore!, then mapped using Bowtie2 to mm10 genome.
The Sam file was converted to a bam file using the Samtools.
DIP-seq data were normalized and generated bigwig files using deepTools.
Assembly: mm10
Supplementary files format and content: bigwig

extract_protocol:
One μg of genomic DNA sheared to 200-500 bp using the LE220 Focused-ultrasonicator (Covaris) was end-repaired and A-tailed. The Illumina PE adapter-ligated DNA was heat-denatured and applied to MeDIP overnight with a monoclonal antibody for 5mC (AnaSpec, Inc.). hMeDIP was performed using a rat monoclonal antibody (Diagenode) for 5hmC. The IP material was recovered with a secondary antibody of rabbit and rat anti-mouse IgG, respectively (Jackson ImmunoResearch) along with protein A/G (Thermo Fisher Scientific), followed by digestion with 20 mg/ml Proteinase K (Invitrogen) for 2 hours.
IP DNA was purified using the MinElute PCR Purification Kit (Qiagen). Confirmation of concentration of 5mC and 5hmC DNA was evaluated by qPCR using positive and negative control primers. The final library amplification was performed using Phusion® hot start II DNA polymerase and 5× Phusion® GC Buffer (Thermo Fisher Scientific) with Illumina paired-end index primers. The PCR-amplified library was size-selected for 220–450-bp fragments on an 8% PAGE gel. The library was normalized based on molarity and pooled for sequencing using v4 ready-to-load reagents for HiSeq 2500 System (Illumina) at 75-bp paired-end reads.

value: Dnmt3a/3b KO


title: PEAT_WL

value: White light


title: Oocytes from primordial follicles, sham, rep 2 [LCMRNA11]

city: Aarhus N

first: Morten

middle: T

last: Veno

state: DK

address: Aabogade 15

country: Denmark

institute: Omiics ApS

description: in vivo

data_processing:
quality filtered and trimmed, and adaptor sequences were removed using  Quality filtering and adaptor removal using trim_galore
Mapping to mouse genome (mm10) using STAR
featureCounts software was used to quantify the number of reads mapped to each gene using gene annotation from Gencode version M25
Assembly: mm10
Supplementary files format and content: tab-delimited text table with raw gene counts for every gene and every sample

source_name: Oocytes from primordial follicles

growth_protocol: In vivo or in vitro. In vitro: alpha-minimal essential medium (α-MEM, Gibco, UK) supplemented with 10% fetal bovine serum (FBS, Gibco).

extract_protocol:
Arcturus® Paradise® Plus RNA Extraction and Isolation Kit (#KIT0312I Arcturus Bioscience Inc., Mountain View, CA, USA) was used for isolation of total cellular RNA from the microdissected cells on the LCM caps, according to the manufacturer’s protocol. RNA from each cap was pooled for the same oocyte stage during extraction. Total cellular RNA from oocytes collected in vivo and in vitro was isolated using Picopure (#KIT0204 Arcturus Bioscience, Inc., Mountain View, CA, USA).
The Ovation® PICO SL WTA System V2 RNA amplification system (#3312 NuGen, Inc., San Carlos, CA, USA) was used for conversion of isolated RNA from the LCM-derived samples to cDNA and linear amplification. Library preparation for microdissected oocytes was performed using an Illumina TruSeq RNA Access kit at BGI, according to the manufacturer’s protocol. RNA sequencing was performed on an Illumina HiSeq platform with two lanes (5 gb per sample). Library preparation for collected oocytes in both groups was performed using the Smart-seq II method, and RNA sequencing was performed using the Illumina HiSeq platform with one lane (5 gb per sample).

value: C57Bl/6j x CBA/J

value: Oocytes from primordial follicles

value: sham


title: Oocytes from primordial follicles, sham, rep 3 [LCMRNA12]

description: in vivo


title: Input

value: human iPSC-derived neurons

value: differentiated neurons

value: input


title: DKO_d7_medip


title: DKO_d0_hmedip


title: Mouse hippocampus from TAC-treated mouse3 [HS1129_S6]

data_processing:
The NextSeq RTA (version 2.4.11.0) was used for base calling. Bcl2fastq (version 2.20.0) was used to convert the .bcl files into .fastq files. Fastq files were aligned to the mouse reference genome (mm10) using HISAT2 software and assembled using StringTie. R package DESeq2 was used for data normalization and differential expression analysis.
Assembly: mm10
Supplementary files format and content: raw counts

source_name: Mouse hippocampal tissue

extract_protocol:
RNA was harvested using TRIzol Reagent (Invitrogen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Mouse was treated with DMSO or TAC

value: Mouse hippocampal tissue

value: WT

value: TAC-treated


title: Oocytes from primordial follicles, sham, rep 1 [LCMRNA10]

description: in vivo


title: Mouse hippocampus from TAC-treated mouse2 [HS1129_S5]


title: DKO_d7_hmedip


title: Mouse hippocampus from DMSO-treated mouse3 [HS1129_S3]

value: DMSO-treated


title: Oocytes from primary follicles, sham, rep 1 [LCMRNA7]

description: in vivo

source_name: Oocytes from primary follicles

value: Oocytes from primary follicles


title: PEAT_90FR

value: 90 minutes FR enriched light


title: Mouse hippocampus from TAC-treated mouse1 [HS1129_S4]


title: Oocytes from primary follicles, sham, rep 2 [LCMRNA8]

description: in vivo


title: Input_ChIP-seq of mus musculus: colonic crypts_rep2

city: PHILADELPHIA

first: Avital

last: Swisa

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

description: Chromatin from isolated colonic crypts was immunoprecipitated with either FOXA1 or FOXA2 antibodies. Libraries were prepared with NEBnext kit for Illumina: DNA samples were blunted and a single 3-end A base was added. Adapters were ligated to the ends of the modified DNA and size selection of 200-bp fragments was performed via PAGE extraction, followed by PCR amplification of 18 cycles.

data_processing:
Basecalls performed using HiSeq Control Software 1.5.15.1, RTA 1.13.48
Data filtering was performed
Alignment was performed using
BigWig files were generated
Peaks were called by HOMER software v4.11.1 on 'factor mode'
Assembly: mm9
Supplementary files format and content: BigWig file
Supplementary files format and content: Peak text file generated by HOMER

source_name: colon

extract_protocol:
Isolated colonic crypts were cross-linked and homogenized in lysis buffer. DNA was sonicated and subjected to immunoprecipitation with FOXA1 or FOXA2 antibodies.
Libraries were prepared with NEBnext kit for Illumina. DNA samples were blunted with a combination of T4 DNA polymerase, Klenow polymerase, and T4 polynucleotide kinase, then a single 3′-end “A” base was added using the Klenow exo (3′-to-5′ exo minus) enzyme. Adapters provided by Illumina were then ligated to the ends of the modified DNA before size selection of ∼200-bp fragments via PAGE extraction. The isolated DNA samples were used as the template for amplification by 18 cycles of PCR.

value: colon

tag: Sex

value: male

value: 3 months

value: Wild type

value: Input


title: Input_ChIP-seq of mus musculus: colonic crypts_rep1


title: FOXA2_ChIP-seq of mus musculus: colonic crypts_rep4


title: FOXA2_ChIP-seq of mus musculus: colonic crypts_rep5


title: FOXA2_ChIP-seq of mus musculus: colonic crypts_rep3


title: Mouse hippocampus from DMSO-treated mouse2 [HS1129_S2]


title: Mouse hippocampus from DMSO-treated mouse1 [HS1129_S1]


title: FOXA2_ChIP-seq of mus musculus: colonic crypts_rep2


title: FOXA1_ChIP-seq of mus musculus: colonic crypts_rep4


title: NC-1

value: embryo

value: ICR

value: NC-FAM


title: FOXA2_ChIP-seq of mus musculus: colonic crypts_rep1


title: Oocytes from primordial follicles, DM, rep 3 [LCMRNA6]

description: in vivo

value: C57Bl/6j x CBA/J

value: Oocytes from primordial follicles

value: DM


title: Oocytes from primordial follicles, DM, rep 2 [LCMRNA5]

description: in vivo


title: FOXA1_ChIP-seq of mus musculus: colonic crypts_rep3


title: FOXA1_ChIP-seq of mus musculus: colonic crypts_rep2


title: sn_RNAseq_mus musculus_97374_rep_2

data_processing:
Raw reads were processed and aligned by Cell Ranger, using “pre-mRNA" reference package to capture unspliced pre-mRNA.
SoupX was first used on a list of abundant and lineage-specific genes ('Muc2', 'Zg16', 'Fcgbp', 'Spink4', 'Tnfaip8', 'Spdef', 'Atoh1', 'Clca1', 'Bcas1') to estimate cell free mRNA contamination and adjust read counts accordingly.
UMIs were removed to within 95% of its confidence interval and cells with >= X% mitochondrial RNA (X being the median+3.0*IQR of mito %) were removed.
Doublets were removed by using DoubletFinder
Assembly: mm10-pre-mRNA
Supplementary files format and content: h5 files of filtered reads
Supplementary files format and content: csv files of gene expression per cell after SoupX filtration and cell information

molecule: nuclear RNA

source_name: distal colon

extract_protocol:
Nuclei were isolated from 1 cm of frozen distal colon tissue from two control mice using Dounce tissue grinder, in Nuclei EZ Lysis Buffer (Sigma, NUC-101).
Libraries were made with Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10X genomics,  PN-1000121,  PN-1000122)

value: distal colon

value: Mixed background

value: 2 month


title: Oocytes from primary follicles, sham, rep 3 [LCMRNA9]

description: in vivo

value: sham


title: Oocytes from primordial follicles, DM, rep 1 [LCMRNA4]

description: in vivo


title: pancreatic mouse islets, pre-diabetic db/db_3, 16-week-old

data_processing:
Sequencing quality was examined by FastQC software and trimmed reads were aligned to mouse and rat mature-tRNA and pre-tRNA sequences from GtRNAdb.
For small RNA sequencing, the sequencing type was 50-bp single-read at 145 M reads.
Unique sequences (considering UMI codes) were counted.
We set the minimum cpm value as at least 5 reads in the smallest library. Only sequences above the minimum cpm value in at least 3 samples were retained.
The remaining reads were aligned to the transcriptome sequences (miRNA, piRNA, rRNA, snRNA, snoRNA).
Assembly: UCSC (http://gtrnadb.ucsc.edu/GtRNAdb2/genomes/eukaryota/Rnorv6/Rnorv6-seq.html)
Supplementary files format and content: raw counts (reads) for each sample.
Supplementary files format and content: transcript per million 1 (TPM1) values for each sample.
Supplementary files format and content: tRF sequences, tRF types, host tRNAs and length, numbers of tRNAs from which the tRFs could originate from, anticodon position  for each sample.
Supplementary files format and content: fold-change and adjusted p values for each sample (cut-off adjusted P ≤ 0.05, FC > 2).

growth_protocol: Mouse pancreatic islets were isolated by collagenase digestion followed by Histopaque density gradient and handpicking.

extract_protocol:
Total RNA from mouse islets was extracted using miRNeasy micro kit (Qiagen # 217084).
Nucleotide modifications were removed from RNA samples prior to sequencing library construction by the following treatments using the rtStar™ tRF&tiRNA Pretreatment kit (Arraystar # AS-FS-005): 3’-aminoacyl (charged) deacylation to 3’-OH for 3’ adaptor ligation, 3’-cP (2’,3’-cyclic phosphate) removal to 3’-OH for 3’ adaptor ligation, 5’-OH (hydroxyl group) phosphorylation to 5’-P for 5’ adaptor ligation, and N1-methyladenosine (m1A), 3-methylcytidine (m3C) and 1-methyl guanosine (m1G) demethylation. 10 ng of total RNA was used for the construction of sequencing cDNA libraries using QIAseq miRNA NGS 48 Index IL kit (Qiagen # 331595) following manufacturers's protocol.

value: pancreatic islets

value: chow diet


title: pancreatic mouse islets, pre-diabetic db/db_2, 16-week-old


title: FOXA2_ChIP-seq of mus musculus: colonic crypts_rep6

value: colon


title: sn_RNAseq_mus musculus_97371_rep_1

value: female


title: RNA-Seq of mus musculus: adult proximal colon of control and FOXA1/2 KO_rep_14

description:
matrix column name: Foxa1/2-rep7-P4799
P4799_RNAseq

data_processing:
Basecalls performed using NextSeq Control Software 2.2.0.4, RTA 2.4.11 or HiSeq Control Software HD 3.4.0.38, RTA 2.7.7 (for distal colon) and NovaSeq Control Software v1.5 (for proximal)
FASTQ files generated using bcl2fastq v2.20.0.422  (for proximal)
The adapter trimming was performed using fastq-mcf program (v1.05) and cutadapt (v2.5).
Kallisto (v0.46.2) was used to pseudoalign samples to the GRCm38 mouse transcriptome without bootstraps.
Kallisto count tables were read into edgeR via TxImport, genes with less than 1 cpm across all samples in one group were removed, and differential gene expression analysis was performed between cell types.
Assembly: mm10
Supplementary files format and content: tsv files with normalized abundance (TPM) for each sample generated by Kallisto and csv matrix table with CPM generated with edgeR

source_name: proximal colon

extract_protocol:
RNA was extracted from 1 cm segments of colonic tissues using TRIzol reagent (Invitrogen, 15596026) and RNeasy Micro Kit (Qiagen, 74004).
Libraries were made with the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, E7530), using the Poly(A) mRNA Magnetic Isolation Module (NEB, E7490)

value: proximal colon

tag: group

value: Villin1-Cre; Foxa1lox/lox; Foxa2lox/lox

value: Female

value: 12 months


title: RNA-Seq of mus musculus: adult proximal colon of control and FOXA1/2 KO_rep_13

description:
matrix column name: Foxa1/2-rep6-P4134
P4134_RNAseq

value: Male

value: 11 months


title: pancreatic mouse islets, het control  db/+_3, 16-week-old


title: Oocytes from primary follicles, DM, rep 2 [LCMRNA2]

description: in vivo

value: C57Bl/6j x CBA/J

value: Oocytes from primary follicles


title: pancreatic mouse islets, het control  db/+_2, 16-week-old


title: pancreatic mouse islets, het control  db/+_1, 16-week-old


title: ChIP-seq_H3K27ac_ILC2_asthma

city: Chiba-shi

first: Arifumi

last: Iwata

address: 1-8-1 Inohana, Chuou-ku

institute: Chiba University

data_processing:
ChIP-seq data were aligned to mm10 genome assembly using Bowtie2 with single-end mode. The data were visualized and the SEs were identified using the HOMER package.
Assembly: mm10
Supplementary files format and content: bedgraph

source_name: Lung

extract_protocol:
Lungs were cut into small pieces and digested in RPMI containing collagenase A and Dnase I using gentleMACS Dissociator and then passed through 70 µm filter. Lung ILC2s and CD4 T cells were sorted by SONY SH800 following crosslink with 1% formaldehyde.
Sonicated samples were immunoprecipitated using H3K27ac antibody (ab4729, Abcam) and Dynabeads Protein A. Chromatin-DNA complexes were washed seven times and reverse-croslinked by overnight incubation at 65 ˚C. DNA fragments were harvested with phenol-chloroform extraction followed by ethanol precipitation. ChIP-seq libraries were prepared with ThruPLEX DNA-seq kit.

treatment_protocol: Mice were administered with 10 µg of HDM at day -6 and day 0-4. Cells were harvested at day 0 for control and day 6 for asthma.

value: WT

value: Lung

value: asthma

value: H3K27ac (abcam, ab4729)


title: Oocytes from primary follicles, DM, rep 1 [LCMRNA1]

description: in vivo

value: DM


title: RNA-Seq of mus musculus: adult proximal colon of control and FOXA1/2 KO_rep_12

description:
matrix column name: Foxa1/2-rep5-P3982
P3982_RNAseq

value: Mixed background

value: 13 months


title: RNA-Seq of mus musculus: adult proximal colon of control and FOXA1/2 KO_rep_11

description:
matrix column name: Foxa1/2-rep4-P3981
P3981_RNAseq

value: 10.5 months


title: ChIP-seq_H3K27ac_CD4T_asthma

value: CD4 T cells


title: ChIP-seq_H3K27ac_ILC2_control

value: control


title: ChIP-seq_H3K27ac_CD4T_control


title: RNA-Seq of mus musculus: adult proximal colon of control and FOXA1/2 KO_rep_10

description:
matrix column name: Foxa1/2-rep3-P3919
P3919_RNAseq

value: proximal colon

value: Villin1-Cre; Foxa1lox/lox; Foxa2lox/lox

value: 10 months


title: TMZ-1500uM-3₋1

city: Tianjin

first: Zhiqiang

last: Liu

address: 22 Qixiangtai Rd

department: Pathophysiology

institute: Tianjin Medical University

data_processing:
The adaptor sequences were trimmed using cutadapt (v1.18) and the untrimmed reads were removed.
sgRNAs were mapped to the annotation file and read count tables were made.
MAGeCK (0.5.8) was used to normalize the count table based on median normalization and fold changes and the significance of the changes in the conditions were calculated for genes and sgRNAs.
Assembly: Homo sapiens hg19
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: brain

growth_protocol: cells were cultured in DMEM medium with 10% FBS.

extract_protocol:
DNA was harvested using DNA isolation kit, and NEB Next® Ultra™ II FS DNA PCR-free Library Prep Kit was used to build database
libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: stable sgRNA-expression U251 cells were treated with 200nM or 1500nM TMZ for 72 hours

value: brain

value: tumor


title: TMZ-1500uM-2₋1


title: TMZ-1500uM-1₋1


title: RNA-Seq of mus musculus: adult proximal colon of control and FOXA1/2 KO_rep_9

description:
matrix column name: Foxa1/2-rep2-P3855
P3855_RNAseq

value: Male

value: 9 months


title: FOXA1_ChIP-seq of mus musculus: colonic crypts_rep1

value: colon

value: male

value: 3 months

value: Wild type


title: Oocytes from primary follicles, DM, rep 3 [LCMRNA3]

description: in vivo

value: C57Bl/6j x CBA/J

value: Oocytes from primary follicles

value: DM


title: TMZ-200uM-3₋1


title: pancreatic mouse islets, pre-diabetic db/db_1, 16-week-old

source_name: pancreatic islets

value: pancreatic islets

value: chow diet


title: RNA-Seq of mus musculus: adult proximal colon of control and FOXA1/2 KO_rep_8

description:
matrix column name: Foxa1/2-rep1-P3854
P3854_RNAseq

value: Mixed background


title: TMZ-200uM-2₋1


title: RNA-Seq of mus musculus: adult proximal colon of control and FOXA1/2 KO_rep_7

description:
matrix column name: Control-rep7-P4636
P4636_RNAseq

value: proximal colon

value: control

value: Foxa1lox/lox; Foxa2lox/lox

value: 18 months


title: TMZ-200uM-1₋1

value: brain

value: tumor


title: embryo25_cell14

city: Edinburgh

first: Lawrence

middle: E

last: Bates

address: Crewe Road

department: Human Genetics Unit

country: United Kingdom

institute: University of Edinburgh

data_processing:
Raw reads were processed as previously (https://doi.org/10.1038/s41467-018-03149-4), aligning to the GRCh38 reference genome using Hisat2 (https://doi.org/10.1038/s41587-019-0201-4).
Gene expression counts were computed from the mapped data using the featureCounts function within RSubread (https://doi.org/10.1093/nar/gkz114).
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file with raw counts for each sample

source_name: Blastocyst

extract_protocol:
Cells were collected directly into 2.5 μl methyltransferase reaction mixture which was comprised of 1 × M.CviPI Reaction buffer, 2 U M.CviPI, 160 μM S-adenosylmethionine, 1 U μl−1 RNAsein, 0.1% IGEPAL then incubated for 15 min at 37 °C. The reaction was stopped and the RNA preserved with the addition of 5 μl RLT plus.
Single-cell RNA sequencing libraries were prepared according to the RNA half of the scNMT-seq protocol (https://doi.org/10.1038/s41467-018-03149-4). Briefly, biotinylated oligo-dT was bound to magnetic beads which were added to single-cell lysates in 96w plates. The captured mRNA was then reverse transcribed and PCR amplified on beads accordingto the Smartseq2 protocol (https://doi.org/10.1038/nprot.2016.138,https://doi.org/10.1038/nprot.2014.006). Indexed Illumina libraries were prepared from the amplified cDNA using Nextera XT reagents and then pooled and sequenced on a HiSeq 2000 instrument using 75bp paired-end reads.

value: Blastocyst

value: ICM

value: WT

tag: developmental stage

value: Male


title: RNA-Seq of mus musculus: adult proximal colon of control and FOXA1/2 KO_rep_6

description:
matrix column name: Control-rep6-P4635
P4635_RNAseq

value: Villin1-Cre; Foxa1lox/lox; Foxa2lox/wt


title: TMZ-0uM-3₋1


title: RNA-Seq of mus musculus: adult proximal colon of control and FOXA1/2 KO_rep_5

description:
matrix column name: Control-rep5-P4634
P4634_RNAseq


title: embryo25_cell13


title: embryo25_cell11


title: TMZ-0uM-2₋1


title: embryo25_cell10